{
"pipeline_id": "haplo-cluster-v1",
"execution_timestamp_utc": "2026-10-29T00:15:00Z",
"total_duration_ms": 3069,
"small_dataset_cohort": {
"cohort_id": "HAPLO-SMALL-URSUS-24",
"cohort_title": "Ursus Holarctic, Arctic & ABC-Islands Peripatric Introgression Panel (24 Specimens / 10 Haplotypes)",
"max_cluster_step_threshold": 4,
"diversity_metrics": {
"total_sequences_n": 24,
"alignment_length_bp": 600,
"unique_haplotypes_h": 10,
"segregating_sites_s": 65,
"parsimony_informative_sites": 62,
"haplotype_diversity_hd": 0.8913,
"haplotype_shannon_entropy_bits": 3.0383,
"nucleotide_diversity_pi": 0.0288,
"watterson_theta_per_site": 0.029,
"tajimas_d": -0.0278,
"selection_demographic_regime": "Structured multi-cluster coalescent Drift-Mutation Equilibrium"
},
"clusters": [
{
"cluster_id": "CLUSTER-01",
"cluster_label": "Ursus arctos (Eurasia-Beringia)",
"hub_haplotype_id": "H01",
"total_samples": 11,
"unique_haplotypes": 4,
"haplotype_ids": [
"H01",
"H03",
"H04",
"H09"
],
"max_internal_step_radius": 2,
"mean_within_cluster_k2p": 0.0028,
"dominant_population": "Eurasia-Beringia"
},
{
"cluster_id": "CLUSTER-02",
"cluster_label": "Ursus maritimus (Arctic-Basin)",
"hub_haplotype_id": "H02",
"total_samples": 10,
"unique_haplotypes": 4,
"haplotype_ids": [
"H02",
"H05",
"H06",
"H10"
],
"max_internal_step_radius": 3,
"mean_within_cluster_k2p": 0.0039,
"dominant_population": "Arctic-Basin"
},
{
"cluster_id": "CLUSTER-03",
"cluster_label": "Ursus americanus (Appalachian-Refugium)",
"hub_haplotype_id": "H07",
"total_samples": 3,
"unique_haplotypes": 2,
"haplotype_ids": [
"H07",
"H08"
],
"max_internal_step_radius": 1,
"mean_within_cluster_k2p": 0.0017,
"dominant_population": "Appalachian-Refugium"
}
],
"haplotypes": [
{
"haplotype_id": "H01",
"cluster_id": "CLUSTER-01",
"sample_count": 6,
"frequency": 0.25,
"primary_taxon": "Ursus arctos",
"subpopulation_counts": {
"Eurasia-Beringia": 6
},
"member_accessions": [
"NC_003427.1_iso01",
"NC_003427.1_iso02",
"NC_003427.1_iso03",
"NC_003427.1_iso04",
"NC_003427.1_iso05",
"NC_003427.1_iso06"
],
"mutations_from_modal_ref": [],
"is_cluster_hub": true,
"sequence": "ATGTTCATAAGCCGGTGATTATTCTCTACGAACCATAAAGACATTGGCACTCTTTACCTTCTGTTCGGTGCATGAGCCGGAATAGTGGGCACTGCCCTCAGCCTTTTAATTCGTGCCGAGCTGGGTCAGCCCGGGGCTCTGTTGGGGGATGATCAGATCTACAATGTAATCGTAACTGCCCATGCATTCGTGATAATCTTCTTCATAGTTATGCCTATTATAATTGGGGGATTCGGGAACTGATTAGTGCCCTTGATGATCGGTGCTCCCGACATAGCGTTCCCTCGAATAAATAACATAAGCTTCTGGTTGCTGCCACCATCTTTCTTACTGCTTCTGGCCTCCTCTATGGTAGAAGCAGGTGCAGGGACTGGATGAACTGTCTATCCTCCTCTAGCGGGTAATCTGGCCCATGCAGGAGCATCGGTAGACTTAACAATCTTTTCTCTGCACCTAGCAGGCATCTCTTCTATTCTGGGGGCTATCAATTTCATCACTACTATTGTTAACATGAAACCCCCTGCAATATCTCAATATCAAACCCCTCTGTTTGTATGATCAGTCCTAATCACAGCAGTACTTCTTCTTTTATCTCTACCA"
},
{
"haplotype_id": "H02",
"cluster_id": "CLUSTER-02",
"sample_count": 5,
"frequency": 0.2083,
"primary_taxon": "Ursus maritimus",
"subpopulation_counts": {
"Arctic-Basin": 5
},
"member_accessions": [
"NC_003428.1_iso01",
"NC_003428.1_iso02",
"NC_003428.1_iso03",
"NC_003428.1_iso04",
"NC_003428.1_iso05"
],
"mutations_from_modal_ref": [
{
"alignment_pos_1based": 11,
"ref_base": "G",
"alt_base": "A",
"label": "G11A"
},
{
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"alt_base": "C",
"label": "T51C"
},
{
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"label": "C57T"
},
{
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"label": "A169G"
},
{
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"alt_base": "T",
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},
{
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},
{
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"label": "T387C"
},
{
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},
{
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},
{
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"label": "A597G"
}
],
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"sequence": "ATGTTCATAAACCGGTGATTATTCTCTACGAACCATAAAGACATTGGCACCCTTTATCTTCTGTTCGGTGCATGAGCCGGAATAGTGGGCACTGCCCTCAGCCTTTTAATTCGTGCCGAGCTGGGTCAGCCCGGGGCTCTGTTGGGGGATGATCAGATCTACAATGTAGTCGTAACTGCCCATGCATTCGTGATAATCTTCTTCATAGTTATGCCTATTATAATTGGGGGATTCGGGAACTGATTAGTGCCTTTGATGATCGGTGCCCCCGACATAGCGTTCCCTCGAATAAATAACATAAGCTTCTGGTTGCTGCCACCATCTTTCTTACTGCTTCTGGCCTCCTCTATGGTAGAAGCAGGTGCAGGGACTGGATGAACTGTCTACCCTCCTCTAGCGGGTAATCTGGCCCATGCAGGAGCATCAGTAGACTTAACAATCTTTTCTCTGCACCTAGCAGGCATCTCTTCTATTCTGGGGGCTATCAATTTCATCACTACTATTATTAACATGAAACCCCCTGCAATATCTCAATATCAAACCCCTCTGTTTGTATGATCAGTCCTAATCACAGCAGTACTTCTTCTTTTATCTCTGCCA"
},
{
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"frequency": 0.0833,
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"subpopulation_counts": {
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},
"member_accessions": [
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"AB086568.1_iso02"
],
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{
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"ref_base": "A",
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"label": "A108G"
}
],
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"sequence": "ATGTTCATAAGCCGGTGATTATTCTCTACGAACCATAAAGACATTGGCACTCTTTACCTTCTGTTCGGTGCATGAGCCGGAATAGTGGGCACTGCCCTCAGCCTTTTGATTCGTGCCGAGCTGGGTCAGCCCGGGGCTCTGTTGGGGGATGATCAGATCTACAATGTAATCGTAACTGCCCATGCATTCGTGATAATCTTCTTCATAGTTATGCCTATTATAATTGGGGGATTCGGGAACTGATTAGTGCCCTTGATGATCGGTGCTCCCGACATAGCGTTCCCTCGAATAAATAACATAAGCTTCTGGTTGCTGCCACCATCTTTCTTACTGCTTCTGGCCTCCTCTATGGTAGAAGCAGGTGCAGGGACTGGATGAACTGTCTATCCTCCTCTAGCGGGTAATCTGGCCCATGCAGGAGCATCGGTAGACTTAACAATCTTTTCTCTGCACCTAGCAGGCATCTCTTCTATTCTGGGGGCTATCAATTTCATCACTACTATTGTTAACATGAAACCCCCTGCAATATCTCAATATCAAACCCCTCTGTTTGTATGATCAGTCCTAATCACAGCAGTACTTCTTCTTTTATCTCTACCA"
},
{
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"cluster_id": "CLUSTER-01",
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},
"member_accessions": [
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{
"alignment_pos_1based": 42,
"ref_base": "C",
"alt_base": "T",
"label": "C42T"
}
],
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"sequence": "ATGTTCATAAGCCGGTGATTATTCTCTACGAACCATAAAGATATTGGCACTCTTTACCTTCTGTTCGGTGCATGAGCCGGAATAGTGGGCACTGCCCTCAGCCTTTTAATTCGTGCCGAGCTGGGTCAGCCCGGGGCTCTGTTGGGGGATGATCAGATCTACAATGTAATCGTAACTGCCCATGCATTCGTGATAATCTTCTTCATAGTTATGCCTATTATAATTGGGGGATTCGGGAACTGATTAGTGCCCTTGATGATCGGTGCTCCCGACATAGCGTTCCCTCGAATAAATAACATAAGCTTCTGGTTGCTGCCACCATCTTTCTTACTGCTTCTGGCCTCCTCTATGGTAGAAGCAGGTGCAGGGACTGGATGAACTGTCTATCCTCCTCTAGCGGGTAATCTGGCCCATGCAGGAGCATCGGTAGACTTAACAATCTTTTCTCTGCACCTAGCAGGCATCTCTTCTATTCTGGGGGCTATCAATTTCATCACTACTATTGTTAACATGAAACCCCCTGCAATATCTCAATATCAAACCCCTCTGTTTGTATGATCAGTCCTAATCACAGCAGTACTTCTTCTTTTATCTCTACCA"
},
{
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},
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{
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},
{
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{
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},
{
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{
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},
{
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{
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{
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],
"is_cluster_hub": true,
"sequence": "ATGTTCATAAATCGATGACTGTTCTCTACAAATCATAAAGATATTGGCACTCTTTACCTTCTGTTCGGTGCATGAGCCGGAATAGTAGGTACTGCTCTCAGCCTTTTAATCCGTGCCGAGCTAGGTCAGCCCGGGGCTCTGTTGGGGGATGATCAAATCTACAATGTAATCGTAACTGCCCATGCATTCGTAATAATCTTCTTTATGGTCATGCCTATTATAATTGGGGGATTTGGGAACTGATTAGTACCCTTAATAATTGGTGCCCCCGACATAGCATTTCCTCGAATAAATAATATAAGTTTCTGACTGCTGCCACCATCTTTCTTATTGCTCCTAGCCTCTTCTATAGTAGAAGCAGGGGCAGGGACTGGATGAACTGTCTACCCCCCTCTAGCGGGTAATCTGGCCCATGCAGGGGCATCAGTAGACTTAACAATCTTTTCTCTACACTTAGCAGGTATCTCTTCTATTCTAGGAGCTATCAATTTCATCACTACTATTATCAACATGAAGCCCCCTGCAATGTCTCAATATCAAACCCCCCTGTTTGTATGATCAGTCCTAATTACGGCAGTGCTTCTTCTTTTATCTCTGCCA"
},
{
"haplotype_id": "H08",
"cluster_id": "CLUSTER-03",
"sample_count": 1,
"frequency": 0.0417,
"primary_taxon": "Ursus americanus",
"subpopulation_counts": {
"Cascadia-Refugium": 1
},
"member_accessions": [
"JX196366.1_iso01"
],
"mutations_from_modal_ref": [
{
"alignment_pos_1based": 11,
"ref_base": "G",
"alt_base": "A",
"label": "G11A"
},
{
"alignment_pos_1based": 12,
"ref_base": "C",
"alt_base": "T",
"label": "C12T"
},
{
"alignment_pos_1based": 15,
"ref_base": "G",
"alt_base": "A",
"label": "G15A"
},
{
"alignment_pos_1based": 19,
"ref_base": "T",
"alt_base": "C",
"label": "T19C"
},
{
"alignment_pos_1based": 21,
"ref_base": "A",
"alt_base": "G",
"label": "A21G"
},
{
"alignment_pos_1based": 30,
"ref_base": "G",
"alt_base": "A",
"label": "G30A"
},
{
"alignment_pos_1based": 33,
"ref_base": "C",
"alt_base": "T",
"label": "C33T"
},
{
"alignment_pos_1based": 42,
"ref_base": "C",
"alt_base": "T",
"label": "C42T"
},
{
"alignment_pos_1based": 84,
"ref_base": "A",
"alt_base": "G",
"label": "A84G"
},
{
"alignment_pos_1based": 87,
"ref_base": "G",
"alt_base": "A",
"label": "G87A"
},
{
"alignment_pos_1based": 90,
"ref_base": "C",
"alt_base": "T",
"label": "C90T"
},
{
"alignment_pos_1based": 96,
"ref_base": "C",
"alt_base": "T",
"label": "C96T"
},
{
"alignment_pos_1based": 111,
"ref_base": "T",
"alt_base": "C",
"label": "T111C"
},
{
"alignment_pos_1based": 123,
"ref_base": "G",
"alt_base": "A",
"label": "G123A"
},
{
"alignment_pos_1based": 156,
"ref_base": "G",
"alt_base": "A",
"label": "G156A"
},
{
"alignment_pos_1based": 192,
"ref_base": "G",
"alt_base": "A",
"label": "G192A"
},
{
"alignment_pos_1based": 204,
"ref_base": "C",
"alt_base": "T",
"label": "C204T"
},
{
"alignment_pos_1based": 207,
"ref_base": "A",
"alt_base": "G",
"label": "A207G"
},
{
"alignment_pos_1based": 210,
"ref_base": "T",
"alt_base": "C",
"label": "T210C"
},
{
"alignment_pos_1based": 234,
"ref_base": "C",
"alt_base": "T",
"label": "C234T"
},
{
"alignment_pos_1based": 249,
"ref_base": "G",
"alt_base": "A",
"label": "G249A"
},
{
"alignment_pos_1based": 255,
"ref_base": "G",
"alt_base": "A",
"label": "G255A"
},
{
"alignment_pos_1based": 258,
"ref_base": "G",
"alt_base": "A",
"label": "G258A"
},
{
"alignment_pos_1based": 261,
"ref_base": "C",
"alt_base": "T",
"label": "C261T"
},
{
"alignment_pos_1based": 267,
"ref_base": "T",
"alt_base": "C",
"label": "T267C"
},
{
"alignment_pos_1based": 279,
"ref_base": "G",
"alt_base": "A",
"label": "G279A"
},
{
"alignment_pos_1based": 282,
"ref_base": "C",
"alt_base": "T",
"label": "C282T"
},
{
"alignment_pos_1based": 297,
"ref_base": "C",
"alt_base": "T",
"label": "C297T"
},
{
"alignment_pos_1based": 303,
"ref_base": "C",
"alt_base": "T",
"label": "C303T"
},
{
"alignment_pos_1based": 309,
"ref_base": "G",
"alt_base": "A",
"label": "G309A"
},
{
"alignment_pos_1based": 310,
"ref_base": "T",
"alt_base": "C",
"label": "T310C"
},
{
"alignment_pos_1based": 331,
"ref_base": "C",
"alt_base": "T",
"label": "C331T"
},
{
"alignment_pos_1based": 336,
"ref_base": "T",
"alt_base": "C",
"label": "T336C"
},
{
"alignment_pos_1based": 339,
"ref_base": "G",
"alt_base": "A",
"label": "G339A"
},
{
"alignment_pos_1based": 345,
"ref_base": "C",
"alt_base": "T",
"label": "C345T"
},
{
"alignment_pos_1based": 351,
"ref_base": "G",
"alt_base": "A",
"label": "G351A"
},
{
"alignment_pos_1based": 363,
"ref_base": "T",
"alt_base": "G",
"label": "T363G"
},
{
"alignment_pos_1based": 387,
"ref_base": "T",
"alt_base": "C",
"label": "T387C"
},
{
"alignment_pos_1based": 390,
"ref_base": "T",
"alt_base": "C",
"label": "T390C"
},
{
"alignment_pos_1based": 420,
"ref_base": "A",
"alt_base": "G",
"label": "A420G"
},
{
"alignment_pos_1based": 426,
"ref_base": "G",
"alt_base": "A",
"label": "G426A"
},
{
"alignment_pos_1based": 450,
"ref_base": "G",
"alt_base": "A",
"label": "G450A"
},
{
"alignment_pos_1based": 454,
"ref_base": "C",
"alt_base": "T",
"label": "C454T"
},
{
"alignment_pos_1based": 462,
"ref_base": "C",
"alt_base": "T",
"label": "C462T"
},
{
"alignment_pos_1based": 477,
"ref_base": "G",
"alt_base": "A",
"label": "G477A"
},
{
"alignment_pos_1based": 480,
"ref_base": "G",
"alt_base": "A",
"label": "G480A"
},
{
"alignment_pos_1based": 505,
"ref_base": "G",
"alt_base": "A",
"label": "G505A"
},
{
"alignment_pos_1based": 507,
"ref_base": "T",
"alt_base": "C",
"label": "T507C"
},
{
"alignment_pos_1based": 516,
"ref_base": "A",
"alt_base": "G",
"label": "A516G"
},
{
"alignment_pos_1based": 528,
"ref_base": "A",
"alt_base": "G",
"label": "A528G"
},
{
"alignment_pos_1based": 546,
"ref_base": "T",
"alt_base": "C",
"label": "T546C"
},
{
"alignment_pos_1based": 570,
"ref_base": "C",
"alt_base": "T",
"label": "C570T"
},
{
"alignment_pos_1based": 573,
"ref_base": "A",
"alt_base": "G",
"label": "A573G"
},
{
"alignment_pos_1based": 579,
"ref_base": "A",
"alt_base": "G",
"label": "A579G"
},
{
"alignment_pos_1based": 597,
"ref_base": "A",
"alt_base": "G",
"label": "A597G"
}
],
"is_cluster_hub": false,
"sequence": "ATGTTCATAAATCGATGACTGTTCTCTACAAATCATAAAGATATTGGCACTCTTTACCTTCTGTTCGGTGCATGAGCCGGAATGGTAGGTACTGCTCTCAGCCTTTTAATCCGTGCCGAGCTAGGTCAGCCCGGGGCTCTGTTGGGGGATGATCAAATCTACAATGTAATCGTAACTGCCCATGCATTCGTAATAATCTTCTTTATGGTCATGCCTATTATAATTGGGGGATTTGGGAACTGATTAGTACCCTTAATAATTGGTGCCCCCGACATAGCATTTCCTCGAATAAATAATATAAGTTTCTGACTGCTGCCACCATCTTTCTTATTGCTCCTAGCCTCTTCTATAGTAGAAGCAGGGGCAGGGACTGGATGAACTGTCTACCCCCCTCTAGCGGGTAATCTGGCCCATGCAGGGGCATCAGTAGACTTAACAATCTTTTCTCTACACTTAGCAGGTATCTCTTCTATTCTAGGAGCTATCAATTTCATCACTACTATTATCAACATGAAGCCCCCTGCAATGTCTCAATATCAAACCCCCCTGTTTGTATGATCAGTCCTAATTACGGCAGTGCTTCTTCTTTTATCTCTGCCA"
},
{
"haplotype_id": "H09",
"cluster_id": "CLUSTER-01",
"sample_count": 1,
"frequency": 0.0417,
"primary_taxon": "Ursus arctos",
"subpopulation_counts": {
"Interior-Alaska": 1
},
"member_accessions": [
"JX196370.1_iso01"
],
"mutations_from_modal_ref": [
{
"alignment_pos_1based": 42,
"ref_base": "C",
"alt_base": "T",
"label": "C42T"
},
{
"alignment_pos_1based": 195,
"ref_base": "A",
"alt_base": "T",
"label": "A195T"
}
],
"is_cluster_hub": false,
"sequence": "ATGTTCATAAGCCGGTGATTATTCTCTACGAACCATAAAGATATTGGCACTCTTTACCTTCTGTTCGGTGCATGAGCCGGAATAGTGGGCACTGCCCTCAGCCTTTTAATTCGTGCCGAGCTGGGTCAGCCCGGGGCTCTGTTGGGGGATGATCAGATCTACAATGTAATCGTAACTGCCCATGCATTCGTGATTATCTTCTTCATAGTTATGCCTATTATAATTGGGGGATTCGGGAACTGATTAGTGCCCTTGATGATCGGTGCTCCCGACATAGCGTTCCCTCGAATAAATAACATAAGCTTCTGGTTGCTGCCACCATCTTTCTTACTGCTTCTGGCCTCCTCTATGGTAGAAGCAGGTGCAGGGACTGGATGAACTGTCTATCCTCCTCTAGCGGGTAATCTGGCCCATGCAGGAGCATCGGTAGACTTAACAATCTTTTCTCTGCACCTAGCAGGCATCTCTTCTATTCTGGGGGCTATCAATTTCATCACTACTATTGTTAACATGAAACCCCCTGCAATATCTCAATATCAAACCCCTCTGTTTGTATGATCAGTCCTAATCACAGCAGTACTTCTTCTTTTATCTCTACCA"
},
{
"haplotype_id": "H10",
"cluster_id": "CLUSTER-02",
"sample_count": 1,
"frequency": 0.0417,
"primary_taxon": "Ursus arctos (ABC Clade)",
"subpopulation_counts": {
"Baranof-Island": 1
},
"member_accessions": [
"JX196392.1_iso01"
],
"mutations_from_modal_ref": [
{
"alignment_pos_1based": 11,
"ref_base": "G",
"alt_base": "A",
"label": "G11A"
},
{
"alignment_pos_1based": 51,
"ref_base": "T",
"alt_base": "C",
"label": "T51C"
},
{
"alignment_pos_1based": 57,
"ref_base": "C",
"alt_base": "T",
"label": "C57T"
},
{
"alignment_pos_1based": 162,
"ref_base": "C",
"alt_base": "T",
"label": "C162T"
},
{
"alignment_pos_1based": 169,
"ref_base": "A",
"alt_base": "G",
"label": "A169G"
},
{
"alignment_pos_1based": 252,
"ref_base": "C",
"alt_base": "T",
"label": "C252T"
},
{
"alignment_pos_1based": 267,
"ref_base": "T",
"alt_base": "C",
"label": "T267C"
},
{
"alignment_pos_1based": 387,
"ref_base": "T",
"alt_base": "C",
"label": "T387C"
},
{
"alignment_pos_1based": 414,
"ref_base": "T",
"alt_base": "C",
"label": "T414C"
},
{
"alignment_pos_1based": 426,
"ref_base": "G",
"alt_base": "A",
"label": "G426A"
},
{
"alignment_pos_1based": 505,
"ref_base": "G",
"alt_base": "A",
"label": "G505A"
},
{
"alignment_pos_1based": 558,
"ref_base": "A",
"alt_base": "G",
"label": "A558G"
},
{
"alignment_pos_1based": 597,
"ref_base": "A",
"alt_base": "G",
"label": "A597G"
}
],
"is_cluster_hub": false,
"sequence": "ATGTTCATAAACCGGTGATTATTCTCTACGAACCATAAAGACATTGGCACCCTTTATCTTCTGTTCGGTGCATGAGCCGGAATAGTGGGCACTGCCCTCAGCCTTTTAATTCGTGCCGAGCTGGGTCAGCCCGGGGCTCTGTTGGGGGATGATCAGATCTATAATGTAGTCGTAACTGCCCATGCATTCGTGATAATCTTCTTCATAGTTATGCCTATTATAATTGGGGGATTCGGGAACTGATTAGTGCCTTTGATGATCGGTGCCCCCGACATAGCGTTCCCTCGAATAAATAACATAAGCTTCTGGTTGCTGCCACCATCTTTCTTACTGCTTCTGGCCTCCTCTATGGTAGAAGCAGGTGCAGGGACTGGATGAACTGTCTACCCTCCTCTAGCGGGTAATCTGGCCCACGCAGGAGCATCAGTAGACTTAACAATCTTTTCTCTGCACCTAGCAGGCATCTCTTCTATTCTGGGGGCTATCAATTTCATCACTACTATTATTAACATGAAACCCCCTGCAATATCTCAATATCAAACCCCTCTGTTTGTATGGTCAGTCCTAATCACAGCAGTACTTCTTCTTTTATCTCTGCCA"
}
],
"msn_edges": [
{
"source_haplotype": "H01",
"target_haplotype": "H03",
"mutational_steps_snps": 1,
"k2p_distance": 0.0017,
"edge_type": "intra-cluster-msn",
"step_mutations": [
"A108G"
]
},
{
"source_haplotype": "H01",
"target_haplotype": "H04",
"mutational_steps_snps": 1,
"k2p_distance": 0.0017,
"edge_type": "intra-cluster-msn",
"step_mutations": [
"C42T"
]
},
{
"source_haplotype": "H04",
"target_haplotype": "H09",
"mutational_steps_snps": 1,
"k2p_distance": 0.0017,
"edge_type": "intra-cluster-msn",
"step_mutations": [
"A195T"
]
},
{
"source_haplotype": "H01",
"target_haplotype": "H02",
"mutational_steps_snps": 10,
"k2p_distance": 0.017,
"edge_type": "inter-cluster-bridge",
"step_mutations": [
"G11A",
"T51C",
"C57T",
"A169G",
"C252T",
"T267C"
]
},
{
"source_haplotype": "H02",
"target_haplotype": "H05",
"mutational_steps_snps": 1,
"k2p_distance": 0.0017,
"edge_type": "intra-cluster-msn",
"step_mutations": [
"T348C"
]
},
{
"source_haplotype": "H02",
"target_haplotype": "H06",
"mutational_steps_snps": 2,
"k2p_distance": 0.0033,
"edge_type": "intra-cluster-msn",
"step_mutations": [
"C162T",
"T414C"
]
},
{
"source_haplotype": "H06",
"target_haplotype": "H10",
"mutational_steps_snps": 1,
"k2p_distance": 0.0017,
"edge_type": "intra-cluster-msn",
"step_mutations": [
"A558G"
]
},
{
"source_haplotype": "H02",
"target_haplotype": "H07",
"mutational_steps_snps": 52,
"k2p_distance": 0.095,
"edge_type": "inter-cluster-bridge",
"step_mutations": [
"C12T",
"G15A",
"T19C",
"A21G",
"G30A",
"C33T"
]
},
{
"source_haplotype": "H07",
"target_haplotype": "H08",
"mutational_steps_snps": 1,
"k2p_distance": 0.0017,
"edge_type": "intra-cluster-msn",
"step_mutations": [
"A84G"
]
},
{
"source_haplotype": "H01",
"target_haplotype": "H09",
"mutational_steps_snps": 2,
"k2p_distance": 0.0033,
"edge_type": "reticulation-loop",
"step_mutations": [
"C42T",
"A195T"
]
},
{
"source_haplotype": "H03",
"target_haplotype": "H04",
"mutational_steps_snps": 2,
"k2p_distance": 0.0033,
"edge_type": "reticulation-loop",
"step_mutations": [
"C42T",
"G108A"
]
}
],
"segregating_columns_1based": [
11,
12,
15,
19,
21,
30,
33,
42,
51,
57,
84,
87,
90,
96,
108,
111,
123,
156,
162,
169,
192,
195,
204,
207,
210,
234,
249,
252,
255,
258,
261,
267,
279,
282,
297,
303,
309,
310,
331,
336,
339,
345,
348,
351,
363,
387,
390,
414,
420,
426,
450,
454,
462,
477,
480,
505,
507,
516,
528,
546,
558,
570,
573,
579,
597
],
"visualizations": {
"dataset_scale_tier": "Small-Dataset Detailed ASCII Mode (h = 10 <= 30 unique haplotypes)",
"recommended_primary_view": "Clean ASCII Haplotype Cluster Viewpoint + Dot-Identity Polymorphic Alignment Matrix",
"ascii_cluster_network_viewpoint": "========================================================================================\nHAPLOTYPE CLUSTER VIEWPOINT: Ursus Holarctic, Arctic & ABC-Islands Peripatric Introgression Panel (24 Specimens / 10 Haplotypes)\nN = 24 seqs | h = 10 haplotypes | S = 65 SNPs | Hd = 0.8913 | pi = 0.0288 | Tajima's D = -0.0278\nClustering Threshold: <= 4 mutational steps (TCS / Minimum Spanning Network)\n========================================================================================\n\n╔══ CLUSTER-01 : Ursus arctos (Eurasia-Beringia) [n = 11 samples | 4 haplotypes | max radius = 2 SNPs] ══╗\n║ ★ HUB (H01) ██████ n=6 ( 25.0%) Taxon: Ursus arctos [NC_003427.1_iso01]\n║ ╠═─(● 1 step)─► (H03) ▓▓ n=2 ( 8.3%) | Ursus arctos | SNPs: [A108G]\n║ ╠═─(● 1 step)─► (H04) ▓▓ n=2 ( 8.3%) | Ursus arctos | SNPs: [C42T]\n║ ╚═─(●● 2 steps)─► (H09) ▓ n=1 ( 4.2%) | Ursus arctos | SNPs: [C42T, A195T]\n╚══════════════════════════════════════════════════════════════════════════════════════╝\n │\n ▼ INTER-CLUSTER MSN BRIDGE: H01 <═══[ 10 Mutational Steps ]═══> H02\n │\n╔══ CLUSTER-02 : Ursus maritimus (Arctic-Basin) [n = 10 samples | 4 haplotypes | max radius = 3 SNPs] ══╗\n║ ★ HUB (H02) █████ n=5 ( 20.8%) Taxon: Ursus maritimus [NC_003428.1_iso01]\n║ ╠═─(● 1 step)─► (H05) ▓▓ n=2 ( 8.3%) | Ursus maritimus | SNPs: [T348C]\n║ ╠═─(●● 2 steps)─► (H06) ▓▓ n=2 ( 8.3%) | Ursus arctos (ABC Clade) | SNPs: [C162T, T414C]\n║ ╚═─(●●● 3 steps)─► (H10) ▓ n=1 ( 4.2%) | Ursus arctos (ABC Clade) | SNPs: [C162T, T414C, A558G]\n╚══════════════════════════════════════════════════════════════════════════════════════╝\n │\n ▼ INTER-CLUSTER MSN BRIDGE: H02 <═══[ 52 Mutational Steps ]═══> H07\n │\n╔══ CLUSTER-03 : Ursus americanus (Appalachian-Refugium) [n = 3 samples | 2 haplotypes | max radius = 1 SNPs] ══╗\n║ ★ HUB (H07) ██ n=2 ( 8.3%) Taxon: Ursus americanus [NC_003426.1_iso01]\n║ ╚═─(● 1 step)─► (H08) ▓ n=1 ( 4.2%) | Ursus americanus | SNPs: [A84G]\n╚══════════════════════════════════════════════════════════════════════════════════════╝\n",
"ascii_polymorphic_site_matrix": "POLYMORPHIC SEGREGATING SITES ALIGNMENT (Showing 36 of 65 variable columns; '.' = matches modal ref H01)\nHaplotype Cluster n Freq% Variable Nucleotide Positions (1-based column index)\n--------- ---------- -- ----- 000000000000001111111122222222222223\n 111123345588990125669900134555667890\n 125910321747068136292547049258179273\n--------- ---------- -- ----- ------------------------------------\nH01 CLUSTER-01 6 25.0 GCGTAGCCTCAGCCATGGCAGACATCGCGGCTGCCC (Ursus arctos)\nH02 CLUSTER-02 5 20.8 A.......CT.........G.......T...C.... (Ursus maritimus)\nH03 CLUSTER-01 2 8.3 ..............G..................... (Ursus arctos)\nH04 CLUSTER-01 2 8.3 .......T............................ (Ursus arctos)\nH05 CLUSTER-02 2 8.3 A.......CT.........G.......T...C.... (Ursus maritimus)\nH06 CLUSTER-02 2 8.3 A.......CT........TG.......T...C.... (Ursus arctos (ABC Clade))\nH07 CLUSTER-03 2 8.3 ATACGATT...ATT.CAA..A.TGCTA.AATCATTT (Ursus americanus)\nH08 CLUSTER-03 1 4.2 ATACGATT..GATT.CAA..A.TGCTA.AATCATTT (Ursus americanus)\nH09 CLUSTER-01 1 4.2 .......T.............T.............. (Ursus arctos)\nH10 CLUSTER-02 1 4.2 A.......CT........TG.......T...C.... (Ursus arctos (ABC Clade))\n",
"ascii_supercluster_heatmap": "COARSE-GRAINED SUPER-CLUSTER MATRIX (N = 24 sequences collapsed into 3 Hub Clusters)\nCluster ID Hub Samples Haplotypes MaxRadius Dominant Clade / Basin Density\n---------- ---- ------- ---------- --------- ------------------------------ ----------------\nCLUSTER-01 H01 11 4 2 bp Ursus arctos (Eurasia-Beringia ███████████\nCLUSTER-02 H02 10 4 3 bp Ursus maritimus (Arctic-Basin) ██████████\nCLUSTER-03 H07 3 2 1 bp Ursus americanus (Appalachian- ███\n\nPAIRWISE INTER-CLUSTER HUB MUTATIONAL STEP HEATMAP (░ <=3 | ▒ 4-9 | ▓ 10-19 | █ >=20 SNPs):\n CLUSTER-01 CLUSTER-02 CLUSTER-03\nCLUSTER-01 · 0snp ▓ 10snp █ 54snp \nCLUSTER-02 ▓ 10snp · 0snp █ 52snp \nCLUSTER-03 █ 54snp █ 52snp · 0snp \n",
"graphviz_dot_network": "graph HaplotypeMinimumSpanningNetwork {\n layout=neato;\n overlap=false;\n splines=true;\n bgcolor=\"#0b0f17\";\n node [fontname=\"monospace\", fontcolor=\"#f8fafc\", style=\"filled\"];\n edge [fontname=\"monospace\", fontsize=9, fontcolor=\"#94a3b8\"];\n \"H01\" [label=\"H01\\n(n=6)\", width=0.79, fillcolor=\"#38bdf8\", penwidth=2.5];\n \"H02\" [label=\"H02\\n(n=5)\", width=0.75, fillcolor=\"#34d399\", penwidth=2.5];\n \"H03\" [label=\"H03\\n(n=2)\", width=0.60, fillcolor=\"#38bdf8\", penwidth=1.2];\n \"H04\" [label=\"H04\\n(n=2)\", width=0.60, fillcolor=\"#38bdf8\", penwidth=1.2];\n \"H05\" [label=\"H05\\n(n=2)\", width=0.60, fillcolor=\"#34d399\", penwidth=1.2];\n \"H06\" [label=\"H06\\n(n=2)\", width=0.60, fillcolor=\"#34d399\", penwidth=1.2];\n \"H07\" [label=\"H07\\n(n=2)\", width=0.60, fillcolor=\"#f59e0b\", penwidth=2.5];\n \"H08\" [label=\"H08\\n(n=1)\", width=0.53, fillcolor=\"#f59e0b\", penwidth=1.2];\n \"H09\" [label=\"H09\\n(n=1)\", width=0.53, fillcolor=\"#38bdf8\", penwidth=1.2];\n \"H10\" [label=\"H10\\n(n=1)\", width=0.53, fillcolor=\"#34d399\", penwidth=1.2];\n \"H01\" -- \"H03\" [label=\"1 snp\", style=\"solid\", color=\"#64748b\"];\n \"H01\" -- \"H04\" [label=\"1 snp\", style=\"solid\", color=\"#64748b\"];\n \"H04\" -- \"H09\" [label=\"1 snp\", style=\"solid\", color=\"#64748b\"];\n \"H01\" -- \"H02\" [label=\"10 snp\", style=\"bold\", color=\"#64748b\"];\n \"H02\" -- \"H05\" [label=\"1 snp\", style=\"solid\", color=\"#64748b\"];\n \"H02\" -- \"H06\" [label=\"2 snp\", style=\"solid\", color=\"#64748b\"];\n \"H06\" -- \"H10\" [label=\"1 snp\", style=\"solid\", color=\"#64748b\"];\n \"H02\" -- \"H07\" [label=\"52 snp\", style=\"bold\", color=\"#64748b\"];\n \"H07\" -- \"H08\" [label=\"1 snp\", style=\"solid\", color=\"#64748b\"];\n \"H01\" -- \"H09\" [label=\"2 snp\", style=\"dashed\", color=\"#64748b\"];\n \"H03\" -- \"H04\" [label=\"2 snp\", style=\"dashed\", color=\"#64748b\"];\n}\n",
"svg_vector_network": ""
}
},
"large_dataset_cohort": {
"cohort_id": "HAPLO-LARGE-SCOMBRIDAE-120",
"cohort_title": "Global Pelagic Scombridae 5-Basin Mitogenome Panel (120 Specimens / 40 Unique Haplotypes)",
"max_cluster_step_threshold": 3,
"diversity_metrics": {
"total_sequences_n": 120,
"alignment_length_bp": 600,
"unique_haplotypes_h": 40,
"segregating_sites_s": 119,
"parsimony_informative_sites": 119,
"haplotype_diversity_hd": 0.9727,
"haplotype_shannon_entropy_bits": 5.094,
"nucleotide_diversity_pi": 0.0448,
"watterson_theta_per_site": 0.037,
"tajimas_d": 0.6862,
"selection_demographic_regime": "Structured multi-cluster coalescent Drift-Mutation Equilibrium"
},
"clusters": [
{
"cluster_id": "CLUSTER-01",
"cluster_label": "Thunnus thynnus (North-Atlantic-Gyre)",
"hub_haplotype_id": "H01",
"total_samples": 24,
"unique_haplotypes": 8,
"haplotype_ids": [
"H01",
"H06",
"H07",
"H16",
"H17",
"H18",
"H19",
"H20"
],
"max_internal_step_radius": 2,
"mean_within_cluster_k2p": 0.0042,
"dominant_population": "North-Atlantic-Gyre"
},
{
"cluster_id": "CLUSTER-02",
"cluster_label": "Thunnus obesus (Mediterranean-Spawning-Basin)",
"hub_haplotype_id": "H02",
"total_samples": 24,
"unique_haplotypes": 8,
"haplotype_ids": [
"H02",
"H08",
"H09",
"H21",
"H22",
"H23",
"H24",
"H25"
],
"max_internal_step_radius": 2,
"mean_within_cluster_k2p": 0.0042,
"dominant_population": "Mediterranean-Spawning-Basin"
},
{
"cluster_id": "CLUSTER-03",
"cluster_label": "Thunnus orientalis (North-Pacific-Kuroshio)",
"hub_haplotype_id": "H03",
"total_samples": 24,
"unique_haplotypes": 8,
"haplotype_ids": [
"H03",
"H10",
"H11",
"H26",
"H27",
"H28",
"H29",
"H30"
],
"max_internal_step_radius": 2,
"mean_within_cluster_k2p": 0.0042,
"dominant_population": "North-Pacific-Kuroshio"
},
{
"cluster_id": "CLUSTER-04",
"cluster_label": "Thunnus albacares (Indo-Pacific-Warm-Pool)",
"hub_haplotype_id": "H04",
"total_samples": 24,
"unique_haplotypes": 8,
"haplotype_ids": [
"H04",
"H12",
"H13",
"H31",
"H32",
"H33",
"H34",
"H35"
],
"max_internal_step_radius": 2,
"mean_within_cluster_k2p": 0.0042,
"dominant_population": "Indo-Pacific-Warm-Pool"
},
{
"cluster_id": "CLUSTER-05",
"cluster_label": "Thunnus maccoyii (Southern-Ocean-Subantarctic)",
"hub_haplotype_id": "H05",
"total_samples": 24,
"unique_haplotypes": 8,
"haplotype_ids": [
"H05",
"H14",
"H15",
"H36",
"H37",
"H38",
"H39",
"H40"
],
"max_internal_step_radius": 2,
"mean_within_cluster_k2p": 0.0042,
"dominant_population": "Southern-Ocean-Subantarctic"
}
],
"haplotypes": [
{
"haplotype_id": "H01",
"cluster_id": "CLUSTER-01",
"sample_count": 8,
"frequency": 0.0667,
"primary_taxon": "Thunnus thynnus",
"subpopulation_counts": {
"North-Atlantic-Gyre": 8
},
"member_accessions": [
"BASIN1_HUB_01",
"BASIN1_HUB_02",
"BASIN1_HUB_03",
"BASIN1_HUB_04",
"BASIN1_HUB_05",
"BASIN1_HUB_06",
"BASIN1_HUB_07",
"BASIN1_HUB_08"
],
"mutations_from_modal_ref": [],
"is_cluster_hub": true,
"sequence": "GTGGCAATCACACGCTGATTTTTCTCAACCAACCATAAAGACATCGGCACCCTCTATCTAGTATTCGGTGCATGAGCTGGAATAGTTGGCACGGCCTTAAGCTTGCTCATCCGAGCTGAACTAAGCCAACCAGGTGCCCTTCTTGGGGACGACCAGATCTACAATGTAATCGTTACGGCCCATGCCTTCGTAATGATTTTCTTTATAGTAATACCAATTATGATTGGAGGATTTGGAAACTGACTTATTCCTCTAATGATCGGAGCCCCCGACATGGCATTCCCACGAATGAACAACATGAGCTTCTGACTCCTTCCCCCTTCTTTCCTTCTGCTCCTAGCTTCTTCAGGAGTTGAGGCTGGAGCCGGAACCGGTTGAACAGTCTACCCTCCCCTTGCCGGCAACCTAGCCCACGCAGGGGCATCAGTTGACCTAACTATTTTCTCACTTCACTTAGCGGGGGTTTCCTCAATTCTTGGGGCAATTAACTTCATCACAACAATTATCAATATGAAACCTGCAGCTATTTCTCAGTATCAAACACCACTGTTTGTATGAGCTGTACTAATTACAGCTGTTCTTCTCCTACTTTCCCTTCCA"
},
{
"haplotype_id": "H02",
"cluster_id": "CLUSTER-02",
"sample_count": 8,
"frequency": 0.0667,
"primary_taxon": "Thunnus obesus",
"subpopulation_counts": {
"Mediterranean-Spawning-Basin": 8
},
"member_accessions": [
"BASIN2_HUB_01",
"BASIN2_HUB_02",
"BASIN2_HUB_03",
"BASIN2_HUB_04",
"BASIN2_HUB_05",
"BASIN2_HUB_06",
"BASIN2_HUB_07",
"BASIN2_HUB_08"
],
"mutations_from_modal_ref": [
{
"alignment_pos_1based": 126,
"ref_base": "C",
"alt_base": "T",
"label": "C126T"
},
{
"alignment_pos_1based": 139,
"ref_base": "C",
"alt_base": "A",
"label": "C139A"
},
{
"alignment_pos_1based": 152,
"ref_base": "A",
"alt_base": "C",
"label": "A152C"
},
{
"alignment_pos_1based": 165,
"ref_base": "T",
"alt_base": "G",
"label": "T165G"
},
{
"alignment_pos_1based": 178,
"ref_base": "G",
"alt_base": "T",
"label": "G178T"
},
{
"alignment_pos_1based": 191,
"ref_base": "T",
"alt_base": "A",
"label": "T191A"
},
{
"alignment_pos_1based": 204,
"ref_base": "T",
"alt_base": "C",
"label": "T204C"
},
{
"alignment_pos_1based": 217,
"ref_base": "A",
"alt_base": "G",
"label": "A217G"
}
],
"is_cluster_hub": true,
"sequence": "GTGGCAATCACACGCTGATTTTTCTCAACCAACCATAAAGACATCGGCACCCTCTATCTAGTATTCGGTGCATGAGCTGGAATAGTTGGCACGGCCTTAAGCTTGCTCATCCGAGCTGAACTAAGTCAACCAGGTGCCATTCTTGGGGACGCCCAGATCTACAAGGTAATCGTTACGTCCCATGCCTTCGAAATGATTTTCTTCATAGTAATACCAGTTATGATTGGAGGATTTGGAAACTGACTTATTCCTCTAATGATCGGAGCCCCCGACATGGCATTCCCACGAATGAACAACATGAGCTTCTGACTCCTTCCCCCTTCTTTCCTTCTGCTCCTAGCTTCTTCAGGAGTTGAGGCTGGAGCCGGAACCGGTTGAACAGTCTACCCTCCCCTTGCCGGCAACCTAGCCCACGCAGGGGCATCAGTTGACCTAACTATTTTCTCACTTCACTTAGCGGGGGTTTCCTCAATTCTTGGGGCAATTAACTTCATCACAACAATTATCAATATGAAACCTGCAGCTATTTCTCAGTATCAAACACCACTGTTTGTATGAGCTGTACTAATTACAGCTGTTCTTCTCCTACTTTCCCTTCCA"
},
{
"haplotype_id": "H03",
"cluster_id": "CLUSTER-03",
"sample_count": 8,
"frequency": 0.0667,
"primary_taxon": "Thunnus orientalis",
"subpopulation_counts": {
"North-Pacific-Kuroshio": 8
},
"member_accessions": [
"BASIN3_HUB_01",
"BASIN3_HUB_02",
"BASIN3_HUB_03",
"BASIN3_HUB_04",
"BASIN3_HUB_05",
"BASIN3_HUB_06",
"BASIN3_HUB_07",
"BASIN3_HUB_08"
],
"mutations_from_modal_ref": [
{
"alignment_pos_1based": 225,
"ref_base": "T",
"alt_base": "C",
"label": "T225C"
},
{
"alignment_pos_1based": 238,
"ref_base": "A",
"alt_base": "G",
"label": "A238G"
},
{
"alignment_pos_1based": 251,
"ref_base": "C",
"alt_base": "T",
"label": "C251T"
},
{
"alignment_pos_1based": 264,
"ref_base": "A",
"alt_base": "G",
"label": "A264G"
},
{
"alignment_pos_1based": 277,
"ref_base": "G",
"alt_base": "T",
"label": "G277T"
},
{
"alignment_pos_1based": 290,
"ref_base": "T",
"alt_base": "A",
"label": "T290A"
},
{
"alignment_pos_1based": 303,
"ref_base": "C",
"alt_base": "T",
"label": "C303T"
},
{
"alignment_pos_1based": 316,
"ref_base": "C",
"alt_base": "G",
"label": "C316G"
},
{
"alignment_pos_1based": 329,
"ref_base": "T",
"alt_base": "C",
"label": "T329C"
},
{
"alignment_pos_1based": 342,
"ref_base": "T",
"alt_base": "A",
"label": "T342A"
},
{
"alignment_pos_1based": 355,
"ref_base": "G",
"alt_base": "C",
"label": "G355C"
},
{
"alignment_pos_1based": 368,
"ref_base": "G",
"alt_base": "A",
"label": "G368A"
},
{
"alignment_pos_1based": 381,
"ref_base": "A",
"alt_base": "T",
"label": "A381T"
},
{
"alignment_pos_1based": 394,
"ref_base": "C",
"alt_base": "A",
"label": "C394A"
},
{
"alignment_pos_1based": 407,
"ref_base": "T",
"alt_base": "C",
"label": "T407C"
},
{
"alignment_pos_1based": 420,
"ref_base": "G",
"alt_base": "A",
"label": "G420A"
}
],
"is_cluster_hub": true,
"sequence": "GTGGCAATCACACGCTGATTTTTCTCAACCAACCATAAAGACATCGGCACCCTCTATCTAGTATTCGGTGCATGAGCTGGAATAGTTGGCACGGCCTTAAGCTTGCTCATCCGAGCTGAACTAAGCCAACCAGGTGCCCTTCTTGGGGACGACCAGATCTACAATGTAATCGTTACGGCCCATGCCTTCGTAATGATTTTCTTTATAGTAATACCAATTATGATCGGAGGATTTGGAGACTGACTTATTCTTCTAATGATCGGGGCCCCCGACATGTCATTCCCACGAAAGAACAACATGAGTTTCTGACTCCTTGCCCCTTCTTTCCCTCTGCTCCTAGCATCTTCAGGAGTTCAGGCTGGAGCCGAAACCGGTTGAACTGTCTACCCTCCCATTGCCGGCAACCCAGCCCACGCAGGAGCATCAGTTGACCTAACTATTTTCTCACTTCACTTAGCGGGGGTTTCCTCAATTCTTGGGGCAATTAACTTCATCACAACAATTATCAATATGAAACCTGCAGCTATTTCTCAGTATCAAACACCACTGTTTGTATGAGCTGTACTAATTACAGCTGTTCTTCTCCTACTTTCCCTTCCA"
},
{
"haplotype_id": "H04",
"cluster_id": "CLUSTER-04",
"sample_count": 8,
"frequency": 0.0667,
"primary_taxon": "Thunnus albacares",
"subpopulation_counts": {
"Indo-Pacific-Warm-Pool": 8
},
"member_accessions": [
"BASIN4_HUB_01",
"BASIN4_HUB_02",
"BASIN4_HUB_03",
"BASIN4_HUB_04",
"BASIN4_HUB_05",
"BASIN4_HUB_06",
"BASIN4_HUB_07",
"BASIN4_HUB_08"
],
"mutations_from_modal_ref": [
{
"alignment_pos_1based": 13,
"ref_base": "C",
"alt_base": "A",
"label": "C13A"
},
{
"alignment_pos_1based": 26,
"ref_base": "C",
"alt_base": "T",
"label": "C26T"
},
{
"alignment_pos_1based": 39,
"ref_base": "A",
"alt_base": "G",
"label": "A39G"
},
{
"alignment_pos_1based": 52,
"ref_base": "C",
"alt_base": "T",
"label": "C52T"
},
{
"alignment_pos_1based": 333,
"ref_base": "G",
"alt_base": "A",
"label": "G333A"
},
{
"alignment_pos_1based": 346,
"ref_base": "T",
"alt_base": "C",
"label": "T346C"
},
{
"alignment_pos_1based": 359,
"ref_base": "C",
"alt_base": "G",
"label": "C359G"
},
{
"alignment_pos_1based": 372,
"ref_base": "C",
"alt_base": "T",
"label": "C372T"
},
{
"alignment_pos_1based": 385,
"ref_base": "T",
"alt_base": "A",
"label": "T385A"
},
{
"alignment_pos_1based": 398,
"ref_base": "C",
"alt_base": "T",
"label": "C398T"
},
{
"alignment_pos_1based": 411,
"ref_base": "C",
"alt_base": "G",
"label": "C411G"
},
{
"alignment_pos_1based": 424,
"ref_base": "T",
"alt_base": "C",
"label": "T424C"
},
{
"alignment_pos_1based": 437,
"ref_base": "C",
"alt_base": "A",
"label": "C437A"
},
{
"alignment_pos_1based": 450,
"ref_base": "T",
"alt_base": "C",
"label": "T450C"
},
{
"alignment_pos_1based": 463,
"ref_base": "G",
"alt_base": "A",
"label": "G463A"
},
{
"alignment_pos_1based": 476,
"ref_base": "T",
"alt_base": "C",
"label": "T476C"
},
{
"alignment_pos_1based": 489,
"ref_base": "C",
"alt_base": "A",
"label": "C489A"
},
{
"alignment_pos_1based": 502,
"ref_base": "A",
"alt_base": "C",
"label": "A502C"
},
{
"alignment_pos_1based": 515,
"ref_base": "A",
"alt_base": "G",
"label": "A515G"
},
{
"alignment_pos_1based": 528,
"ref_base": "T",
"alt_base": "C",
"label": "T528C"
},
{
"alignment_pos_1based": 541,
"ref_base": "A",
"alt_base": "G",
"label": "A541G"
},
{
"alignment_pos_1based": 554,
"ref_base": "T",
"alt_base": "C",
"label": "T554C"
},
{
"alignment_pos_1based": 567,
"ref_base": "A",
"alt_base": "G",
"label": "A567G"
},
{
"alignment_pos_1based": 580,
"ref_base": "C",
"alt_base": "T",
"label": "C580T"
}
],
"is_cluster_hub": true,
"sequence": "GTGGCAATCACAAGCTGATTTTTCTTAACCAACCATAAGGACATCGGCACCTTCTATCTAGTATTCGGTGCATGAGCTGGAATAGTTGGCACGGCCTTAAGCTTGCTCATCCGAGCTGAACTAAGCCAACCAGGTGCCCTTCTTGGGGACGACCAGATCTACAATGTAATCGTTACGGCCCATGCCTTCGTAATGATTTTCTTTATAGTAATACCAATTATGATTGGAGGATTTGGAAACTGACTTATTCCTCTAATGATCGGAGCCCCCGACATGGCATTCCCACGAATGAACAACATGAGCTTCTGACTCCTTCCCCCTTCTTTCCTTCTACTCCTAGCTTCTCCAGGAGTTGAGGGTGGAGCCGGAACTGGTTGAACAGTCAACCCTCCCCTTGTCGGCAACCTAGCGCACGCAGGGGCACCAGTTGACCTAAATATTTTCTCACTCCACTTAGCGGGGATTTCCTCAATTCCTGGGGCAATTAAATTCATCACAACACTTATCAATATGAGACCTGCAGCTATCTCTCAGTATCAAGCACCACTGTTTGCATGAGCTGTACTGATTACAGCTGTTTTTCTCCTACTTTCCCTTCCA"
},
{
"haplotype_id": "H05",
"cluster_id": "CLUSTER-05",
"sample_count": 8,
"frequency": 0.0667,
"primary_taxon": "Thunnus maccoyii",
"subpopulation_counts": {
"Southern-Ocean-Subantarctic": 8
},
"member_accessions": [
"BASIN5_HUB_01",
"BASIN5_HUB_02",
"BASIN5_HUB_03",
"BASIN5_HUB_04",
"BASIN5_HUB_05",
"BASIN5_HUB_06",
"BASIN5_HUB_07",
"BASIN5_HUB_08"
],
"mutations_from_modal_ref": [
{
"alignment_pos_1based": 17,
"ref_base": "G",
"alt_base": "C",
"label": "G17C"
},
{
"alignment_pos_1based": 30,
"ref_base": "C",
"alt_base": "G",
"label": "C30G"
},
{
"alignment_pos_1based": 43,
"ref_base": "A",
"alt_base": "T",
"label": "A43T"
},
{
"alignment_pos_1based": 56,
"ref_base": "A",
"alt_base": "G",
"label": "A56G"
},
{
"alignment_pos_1based": 69,
"ref_base": "T",
"alt_base": "C",
"label": "T69C"
},
{
"alignment_pos_1based": 82,
"ref_base": "A",
"alt_base": "G",
"label": "A82G"
},
{
"alignment_pos_1based": 95,
"ref_base": "C",
"alt_base": "T",
"label": "C95T"
},
{
"alignment_pos_1based": 108,
"ref_base": "C",
"alt_base": "A",
"label": "C108A"
},
{
"alignment_pos_1based": 121,
"ref_base": "C",
"alt_base": "T",
"label": "C121T"
},
{
"alignment_pos_1based": 134,
"ref_base": "G",
"alt_base": "A",
"label": "G134A"
},
{
"alignment_pos_1based": 147,
"ref_base": "G",
"alt_base": "T",
"label": "G147T"
},
{
"alignment_pos_1based": 160,
"ref_base": "T",
"alt_base": "A",
"label": "T160A"
},
{
"alignment_pos_1based": 173,
"ref_base": "T",
"alt_base": "C",
"label": "T173C"
},
{
"alignment_pos_1based": 186,
"ref_base": "C",
"alt_base": "G",
"label": "C186G"
},
{
"alignment_pos_1based": 199,
"ref_base": "T",
"alt_base": "C",
"label": "T199C"
},
{
"alignment_pos_1based": 212,
"ref_base": "T",
"alt_base": "A",
"label": "T212A"
},
{
"alignment_pos_1based": 225,
"ref_base": "T",
"alt_base": "C",
"label": "T225C"
},
{
"alignment_pos_1based": 238,
"ref_base": "A",
"alt_base": "G",
"label": "A238G"
},
{
"alignment_pos_1based": 251,
"ref_base": "C",
"alt_base": "T",
"label": "C251T"
},
{
"alignment_pos_1based": 264,
"ref_base": "A",
"alt_base": "G",
"label": "A264G"
},
{
"alignment_pos_1based": 441,
"ref_base": "T",
"alt_base": "C",
"label": "T441C"
},
{
"alignment_pos_1based": 454,
"ref_base": "T",
"alt_base": "G",
"label": "T454G"
},
{
"alignment_pos_1based": 467,
"ref_base": "C",
"alt_base": "T",
"label": "C467T"
},
{
"alignment_pos_1based": 480,
"ref_base": "G",
"alt_base": "A",
"label": "G480A"
},
{
"alignment_pos_1based": 493,
"ref_base": "A",
"alt_base": "C",
"label": "A493C"
},
{
"alignment_pos_1based": 506,
"ref_base": "T",
"alt_base": "G",
"label": "T506G"
},
{
"alignment_pos_1based": 519,
"ref_base": "T",
"alt_base": "C",
"label": "T519C"
},
{
"alignment_pos_1based": 532,
"ref_base": "C",
"alt_base": "A",
"label": "C532A"
},
{
"alignment_pos_1based": 545,
"ref_base": "C",
"alt_base": "T",
"label": "C545T"
},
{
"alignment_pos_1based": 558,
"ref_base": "A",
"alt_base": "G",
"label": "A558G"
},
{
"alignment_pos_1based": 571,
"ref_base": "A",
"alt_base": "T",
"label": "A571T"
},
{
"alignment_pos_1based": 584,
"ref_base": "T",
"alt_base": "A",
"label": "T584A"
}
],
"is_cluster_hub": true,
"sequence": "GTGGCAATCACACGCTCATTTTTCTCAACGAACCATAAAGACTTCGGCACCCTCTGTCTAGTATTCGGCGCATGAGCTGGAGTAGTTGGCACGGTCTTAAGCTTGCTAATCCGAGCTGAATTAAGCCAACCAGATGCCCTTCTTGGTGACGACCAGATCAACAATGTAATCGCTACGGCCCATGCGTTCGTAATGATTCTCTTTATAGTAAAACCAATTATGATCGGAGGATTTGGAGACTGACTTATTCTTCTAATGATCGGGGCCCCCGACATGGCATTCCCACGAATGAACAACATGAGCTTCTGACTCCTTCCCCCTTCTTTCCTTCTGCTCCTAGCTTCTTCAGGAGTTGAGGCTGGAGCCGGAACCGGTTGAACAGTCTACCCTCCCCTTGCCGGCAACCTAGCCCACGCAGGGGCATCAGTTGACCTAACTATCTTCTCACTTCACGTAGCGGGGGTTTTCTCAATTCTTGGAGCAATTAACTTCCTCACAACAATTAGCAATATGAAACCCGCAGCTATTTCTAAGTATCAAACACTACTGTTTGTATGGGCTGTACTAATTTCAGCTGTTCTTCACCTACTTTCCCTTCCA"
},
{
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"frequency": 0.025,
"primary_taxon": "Thunnus thynnus",
"subpopulation_counts": {
"North-Atlantic-Gyre": 3
},
"member_accessions": [
"BASIN1_SAT1_01",
"BASIN1_SAT1_02",
"BASIN1_SAT1_03"
],
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{
"alignment_pos_1based": 42,
"ref_base": "C",
"alt_base": "T",
"label": "C42T"
}
],
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"sequence": "GTGGCAATCACACGCTGATTTTTCTCAACCAACCATAAAGATATCGGCACCCTCTATCTAGTATTCGGTGCATGAGCTGGAATAGTTGGCACGGCCTTAAGCTTGCTCATCCGAGCTGAACTAAGCCAACCAGGTGCCCTTCTTGGGGACGACCAGATCTACAATGTAATCGTTACGGCCCATGCCTTCGTAATGATTTTCTTTATAGTAATACCAATTATGATTGGAGGATTTGGAAACTGACTTATTCCTCTAATGATCGGAGCCCCCGACATGGCATTCCCACGAATGAACAACATGAGCTTCTGACTCCTTCCCCCTTCTTTCCTTCTGCTCCTAGCTTCTTCAGGAGTTGAGGCTGGAGCCGGAACCGGTTGAACAGTCTACCCTCCCCTTGCCGGCAACCTAGCCCACGCAGGGGCATCAGTTGACCTAACTATTTTCTCACTTCACTTAGCGGGGGTTTCCTCAATTCTTGGGGCAATTAACTTCATCACAACAATTATCAATATGAAACCTGCAGCTATTTCTCAGTATCAAACACCACTGTTTGTATGAGCTGTACTAATTACAGCTGTTCTTCTCCTACTTTCCCTTCCA"
},
{
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},
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"BASIN1_SAT2_02",
"BASIN1_SAT2_03"
],
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{
"alignment_pos_1based": 71,
"ref_base": "C",
"alt_base": "T",
"label": "C71T"
}
],
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"sequence": "GTGGCAATCACACGCTGATTTTTCTCAACCAACCATAAAGACATCGGCACCCTCTATCTAGTATTCGGTGTATGAGCTGGAATAGTTGGCACGGCCTTAAGCTTGCTCATCCGAGCTGAACTAAGCCAACCAGGTGCCCTTCTTGGGGACGACCAGATCTACAATGTAATCGTTACGGCCCATGCCTTCGTAATGATTTTCTTTATAGTAATACCAATTATGATTGGAGGATTTGGAAACTGACTTATTCCTCTAATGATCGGAGCCCCCGACATGGCATTCCCACGAATGAACAACATGAGCTTCTGACTCCTTCCCCCTTCTTTCCTTCTGCTCCTAGCTTCTTCAGGAGTTGAGGCTGGAGCCGGAACCGGTTGAACAGTCTACCCTCCCCTTGCCGGCAACCTAGCCCACGCAGGGGCATCAGTTGACCTAACTATTTTCTCACTTCACTTAGCGGGGGTTTCCTCAATTCTTGGGGCAATTAACTTCATCACAACAATTATCAATATGAAACCTGCAGCTATTTCTCAGTATCAAACACCACTGTTTGTATGAGCTGTACTAATTACAGCTGTTCTTCTCCTACTTTCCCTTCCA"
},
{
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},
"member_accessions": [
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"BASIN2_SAT1_02",
"BASIN2_SAT1_03"
],
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{
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"ref_base": "G",
"alt_base": "A",
"label": "G115A"
},
{
"alignment_pos_1based": 126,
"ref_base": "C",
"alt_base": "T",
"label": "C126T"
},
{
"alignment_pos_1based": 139,
"ref_base": "C",
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},
{
"alignment_pos_1based": 152,
"ref_base": "A",
"alt_base": "C",
"label": "A152C"
},
{
"alignment_pos_1based": 165,
"ref_base": "T",
"alt_base": "G",
"label": "T165G"
},
{
"alignment_pos_1based": 178,
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},
{
"alignment_pos_1based": 191,
"ref_base": "T",
"alt_base": "A",
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},
{
"alignment_pos_1based": 204,
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{
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"label": "A217G"
}
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},
{
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},
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"BASIN2_SAT2_02",
"BASIN2_SAT2_03"
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},
{
"alignment_pos_1based": 139,
"ref_base": "C",
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},
{
"alignment_pos_1based": 144,
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},
{
"alignment_pos_1based": 152,
"ref_base": "A",
"alt_base": "C",
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},
{
"alignment_pos_1based": 165,
"ref_base": "T",
"alt_base": "G",
"label": "T165G"
},
{
"alignment_pos_1based": 178,
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},
{
"alignment_pos_1based": 191,
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},
{
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{
"alignment_pos_1based": 217,
"ref_base": "A",
"alt_base": "G",
"label": "A217G"
}
],
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"sequence": "GTGGCAATCACACGCTGATTTTTCTCAACCAACCATAAAGACATCGGCACCCTCTATCTAGTATTCGGTGCATGAGCTGGAATAGTTGGCACGGCCTTAAGCTTGCTCATCCGAGCTGAACTAAGTCAACCAGGTGCCATTCTCGGGGACGCCCAGATCTACAAGGTAATCGTTACGTCCCATGCCTTCGAAATGATTTTCTTCATAGTAATACCAGTTATGATTGGAGGATTTGGAAACTGACTTATTCCTCTAATGATCGGAGCCCCCGACATGGCATTCCCACGAATGAACAACATGAGCTTCTGACTCCTTCCCCCTTCTTTCCTTCTGCTCCTAGCTTCTTCAGGAGTTGAGGCTGGAGCCGGAACCGGTTGAACAGTCTACCCTCCCCTTGCCGGCAACCTAGCCCACGCAGGGGCATCAGTTGACCTAACTATTTTCTCACTTCACTTAGCGGGGGTTTCCTCAATTCTTGGGGCAATTAACTTCATCACAACAATTATCAATATGAAACCTGCAGCTATTTCTCAGTATCAAACACCACTGTTTGTATGAGCTGTACTAATTACAGCTGTTCTTCTCCTACTTTCCCTTCCA"
},
{
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"subpopulation_counts": {
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},
"member_accessions": [
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"BASIN3_SAT1_02",
"BASIN3_SAT1_03"
],
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{
"alignment_pos_1based": 188,
"ref_base": "T",
"alt_base": "C",
"label": "T188C"
},
{
"alignment_pos_1based": 225,
"ref_base": "T",
"alt_base": "C",
"label": "T225C"
},
{
"alignment_pos_1based": 238,
"ref_base": "A",
"alt_base": "G",
"label": "A238G"
},
{
"alignment_pos_1based": 251,
"ref_base": "C",
"alt_base": "T",
"label": "C251T"
},
{
"alignment_pos_1based": 264,
"ref_base": "A",
"alt_base": "G",
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},
{
"alignment_pos_1based": 277,
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"label": "G277T"
},
{
"alignment_pos_1based": 290,
"ref_base": "T",
"alt_base": "A",
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},
{
"alignment_pos_1based": 303,
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},
{
"alignment_pos_1based": 316,
"ref_base": "C",
"alt_base": "G",
"label": "C316G"
},
{
"alignment_pos_1based": 329,
"ref_base": "T",
"alt_base": "C",
"label": "T329C"
},
{
"alignment_pos_1based": 342,
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"alt_base": "A",
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},
{
"alignment_pos_1based": 355,
"ref_base": "G",
"alt_base": "C",
"label": "G355C"
},
{
"alignment_pos_1based": 368,
"ref_base": "G",
"alt_base": "A",
"label": "G368A"
},
{
"alignment_pos_1based": 381,
"ref_base": "A",
"alt_base": "T",
"label": "A381T"
},
{
"alignment_pos_1based": 394,
"ref_base": "C",
"alt_base": "A",
"label": "C394A"
},
{
"alignment_pos_1based": 407,
"ref_base": "T",
"alt_base": "C",
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},
{
"alignment_pos_1based": 420,
"ref_base": "G",
"alt_base": "A",
"label": "G420A"
}
],
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},
{
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},
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"BASIN3_SAT2_02",
"BASIN3_SAT2_03"
],
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{
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"ref_base": "A",
"alt_base": "G",
"label": "A217G"
},
{
"alignment_pos_1based": 225,
"ref_base": "T",
"alt_base": "C",
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},
{
"alignment_pos_1based": 238,
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},
{
"alignment_pos_1based": 251,
"ref_base": "C",
"alt_base": "T",
"label": "C251T"
},
{
"alignment_pos_1based": 264,
"ref_base": "A",
"alt_base": "G",
"label": "A264G"
},
{
"alignment_pos_1based": 277,
"ref_base": "G",
"alt_base": "T",
"label": "G277T"
},
{
"alignment_pos_1based": 290,
"ref_base": "T",
"alt_base": "A",
"label": "T290A"
},
{
"alignment_pos_1based": 303,
"ref_base": "C",
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},
{
"alignment_pos_1based": 316,
"ref_base": "C",
"alt_base": "G",
"label": "C316G"
},
{
"alignment_pos_1based": 329,
"ref_base": "T",
"alt_base": "C",
"label": "T329C"
},
{
"alignment_pos_1based": 342,
"ref_base": "T",
"alt_base": "A",
"label": "T342A"
},
{
"alignment_pos_1based": 355,
"ref_base": "G",
"alt_base": "C",
"label": "G355C"
},
{
"alignment_pos_1based": 368,
"ref_base": "G",
"alt_base": "A",
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},
{
"alignment_pos_1based": 381,
"ref_base": "A",
"alt_base": "T",
"label": "A381T"
},
{
"alignment_pos_1based": 394,
"ref_base": "C",
"alt_base": "A",
"label": "C394A"
},
{
"alignment_pos_1based": 407,
"ref_base": "T",
"alt_base": "C",
"label": "T407C"
},
{
"alignment_pos_1based": 420,
"ref_base": "G",
"alt_base": "A",
"label": "G420A"
}
],
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"sequence": "GTGGCAATCACACGCTGATTTTTCTCAACCAACCATAAAGACATCGGCACCCTCTATCTAGTATTCGGTGCATGAGCTGGAATAGTTGGCACGGCCTTAAGCTTGCTCATCCGAGCTGAACTAAGCCAACCAGGTGCCCTTCTTGGGGACGACCAGATCTACAATGTAATCGTTACGGCCCATGCCTTCGTAATGATTTTCTTTATAGTAATACCAGTTATGATCGGAGGATTTGGAGACTGACTTATTCTTCTAATGATCGGGGCCCCCGACATGTCATTCCCACGAAAGAACAACATGAGTTTCTGACTCCTTGCCCCTTCTTTCCCTCTGCTCCTAGCATCTTCAGGAGTTCAGGCTGGAGCCGAAACCGGTTGAACTGTCTACCCTCCCATTGCCGGCAACCCAGCCCACGCAGGAGCATCAGTTGACCTAACTATTTTCTCACTTCACTTAGCGGGGGTTTCCTCAATTCTTGGGGCAATTAACTTCATCACAACAATTATCAATATGAAACCTGCAGCTATTTCTCAGTATCAAACACCACTGTTTGTATGAGCTGTACTAATTACAGCTGTTCTTCTCCTACTTTCCCTTCCA"
},
{
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"frequency": 0.025,
"primary_taxon": "Thunnus albacares",
"subpopulation_counts": {
"Indo-Pacific-Warm-Pool": 3
},
"member_accessions": [
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"BASIN4_SAT1_02",
"BASIN4_SAT1_03"
],
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{
"alignment_pos_1based": 13,
"ref_base": "C",
"alt_base": "A",
"label": "C13A"
},
{
"alignment_pos_1based": 26,
"ref_base": "C",
"alt_base": "T",
"label": "C26T"
},
{
"alignment_pos_1based": 39,
"ref_base": "A",
"alt_base": "G",
"label": "A39G"
},
{
"alignment_pos_1based": 52,
"ref_base": "C",
"alt_base": "T",
"label": "C52T"
},
{
"alignment_pos_1based": 261,
"ref_base": "C",
"alt_base": "T",
"label": "C261T"
},
{
"alignment_pos_1based": 333,
"ref_base": "G",
"alt_base": "A",
"label": "G333A"
},
{
"alignment_pos_1based": 346,
"ref_base": "T",
"alt_base": "C",
"label": "T346C"
},
{
"alignment_pos_1based": 359,
"ref_base": "C",
"alt_base": "G",
"label": "C359G"
},
{
"alignment_pos_1based": 372,
"ref_base": "C",
"alt_base": "T",
"label": "C372T"
},
{
"alignment_pos_1based": 385,
"ref_base": "T",
"alt_base": "A",
"label": "T385A"
},
{
"alignment_pos_1based": 398,
"ref_base": "C",
"alt_base": "T",
"label": "C398T"
},
{
"alignment_pos_1based": 411,
"ref_base": "C",
"alt_base": "G",
"label": "C411G"
},
{
"alignment_pos_1based": 424,
"ref_base": "T",
"alt_base": "C",
"label": "T424C"
},
{
"alignment_pos_1based": 437,
"ref_base": "C",
"alt_base": "A",
"label": "C437A"
},
{
"alignment_pos_1based": 450,
"ref_base": "T",
"alt_base": "C",
"label": "T450C"
},
{
"alignment_pos_1based": 463,
"ref_base": "G",
"alt_base": "A",
"label": "G463A"
},
{
"alignment_pos_1based": 476,
"ref_base": "T",
"alt_base": "C",
"label": "T476C"
},
{
"alignment_pos_1based": 489,
"ref_base": "C",
"alt_base": "A",
"label": "C489A"
},
{
"alignment_pos_1based": 502,
"ref_base": "A",
"alt_base": "C",
"label": "A502C"
},
{
"alignment_pos_1based": 515,
"ref_base": "A",
"alt_base": "G",
"label": "A515G"
},
{
"alignment_pos_1based": 528,
"ref_base": "T",
"alt_base": "C",
"label": "T528C"
},
{
"alignment_pos_1based": 541,
"ref_base": "A",
"alt_base": "G",
"label": "A541G"
},
{
"alignment_pos_1based": 554,
"ref_base": "T",
"alt_base": "C",
"label": "T554C"
},
{
"alignment_pos_1based": 567,
"ref_base": "A",
"alt_base": "G",
"label": "A567G"
},
{
"alignment_pos_1based": 580,
"ref_base": "C",
"alt_base": "T",
"label": "C580T"
}
],
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"sequence": "GTGGCAATCACAAGCTGATTTTTCTTAACCAACCATAAGGACATCGGCACCTTCTATCTAGTATTCGGTGCATGAGCTGGAATAGTTGGCACGGCCTTAAGCTTGCTCATCCGAGCTGAACTAAGCCAACCAGGTGCCCTTCTTGGGGACGACCAGATCTACAATGTAATCGTTACGGCCCATGCCTTCGTAATGATTTTCTTTATAGTAATACCAATTATGATTGGAGGATTTGGAAACTGACTTATTCCTCTAATGATTGGAGCCCCCGACATGGCATTCCCACGAATGAACAACATGAGCTTCTGACTCCTTCCCCCTTCTTTCCTTCTACTCCTAGCTTCTCCAGGAGTTGAGGGTGGAGCCGGAACTGGTTGAACAGTCAACCCTCCCCTTGTCGGCAACCTAGCGCACGCAGGGGCACCAGTTGACCTAAATATTTTCTCACTCCACTTAGCGGGGATTTCCTCAATTCCTGGGGCAATTAAATTCATCACAACACTTATCAATATGAGACCTGCAGCTATCTCTCAGTATCAAGCACCACTGTTTGCATGAGCTGTACTGATTACAGCTGTTTTTCTCCTACTTTCCCTTCCA"
},
{
"haplotype_id": "H13",
"cluster_id": "CLUSTER-04",
"sample_count": 3,
"frequency": 0.025,
"primary_taxon": "Thunnus albacares",
"subpopulation_counts": {
"Indo-Pacific-Warm-Pool": 3
},
"member_accessions": [
"BASIN4_SAT2_01",
"BASIN4_SAT2_02",
"BASIN4_SAT2_03"
],
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{
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{
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{
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{
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{
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"ref_base": "C",
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{
"alignment_pos_1based": 424,
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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},
{
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{
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{
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{
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{
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},
{
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{
"alignment_pos_1based": 363,
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{
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{
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{
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{
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{
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{
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},
{
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{
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},
{
"alignment_pos_1based": 545,
"ref_base": "C",
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},
{
"alignment_pos_1based": 558,
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},
{
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{
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},
{
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"frequency": 0.0167,
"primary_taxon": "Thunnus thynnus",
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},
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"BASIN1_SAT3_02"
],
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{
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"ref_base": "A",
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}
],
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},
{
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},
"member_accessions": [
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"BASIN1_SAT4_02"
],
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{
"alignment_pos_1based": 129,
"ref_base": "A",
"alt_base": "G",
"label": "A129G"
}
],
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"sequence": "GTGGCAATCACACGCTGATTTTTCTCAACCAACCATAAAGACATCGGCACCCTCTATCTAGTATTCGGTGCATGAGCTGGAATAGTTGGCACGGCCTTAAGCTTGCTCATCCGAGCTGAACTAAGCCAGCCAGGTGCCCTTCTTGGGGACGACCAGATCTACAATGTAATCGTTACGGCCCATGCCTTCGTAATGATTTTCTTTATAGTAATACCAATTATGATTGGAGGATTTGGAAACTGACTTATTCCTCTAATGATCGGAGCCCCCGACATGGCATTCCCACGAATGAACAACATGAGCTTCTGACTCCTTCCCCCTTCTTTCCTTCTGCTCCTAGCTTCTTCAGGAGTTGAGGCTGGAGCCGGAACCGGTTGAACAGTCTACCCTCCCCTTGCCGGCAACCTAGCCCACGCAGGGGCATCAGTTGACCTAACTATTTTCTCACTTCACTTAGCGGGGGTTTCCTCAATTCTTGGGGCAATTAACTTCATCACAACAATTATCAATATGAAACCTGCAGCTATTTCTCAGTATCAAACACCACTGTTTGTATGAGCTGTACTAATTACAGCTGTTCTTCTCCTACTTTCCCTTCCA"
},
{
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},
"member_accessions": [
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"BASIN1_SAT5_02"
],
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{
"alignment_pos_1based": 158,
"ref_base": "T",
"alt_base": "C",
"label": "T158C"
},
{
"alignment_pos_1based": 227,
"ref_base": "G",
"alt_base": "A",
"label": "G227A"
}
],
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"sequence": "GTGGCAATCACACGCTGATTTTTCTCAACCAACCATAAAGACATCGGCACCCTCTATCTAGTATTCGGTGCATGAGCTGGAATAGTTGGCACGGCCTTAAGCTTGCTCATCCGAGCTGAACTAAGCCAACCAGGTGCCCTTCTTGGGGACGACCAGACCTACAATGTAATCGTTACGGCCCATGCCTTCGTAATGATTTTCTTTATAGTAATACCAATTATGATTGAAGGATTTGGAAACTGACTTATTCCTCTAATGATCGGAGCCCCCGACATGGCATTCCCACGAATGAACAACATGAGCTTCTGACTCCTTCCCCCTTCTTTCCTTCTGCTCCTAGCTTCTTCAGGAGTTGAGGCTGGAGCCGGAACCGGTTGAACAGTCTACCCTCCCCTTGCCGGCAACCTAGCCCACGCAGGGGCATCAGTTGACCTAACTATTTTCTCACTTCACTTAGCGGGGGTTTCCTCAATTCTTGGGGCAATTAACTTCATCACAACAATTATCAATATGAAACCTGCAGCTATTTCTCAGTATCAAACACCACTGTTTGTATGAGCTGTACTAATTACAGCTGTTCTTCTCCTACTTTCCCTTCCA"
},
{
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},
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"BASIN1_SAT6_02"
],
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{
"alignment_pos_1based": 187,
"ref_base": "T",
"alt_base": "C",
"label": "T187C"
},
{
"alignment_pos_1based": 256,
"ref_base": "A",
"alt_base": "C",
"label": "A256C"
}
],
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"sequence": "GTGGCAATCACACGCTGATTTTTCTCAACCAACCATAAAGACATCGGCACCCTCTATCTAGTATTCGGTGCATGAGCTGGAATAGTTGGCACGGCCTTAAGCTTGCTCATCCGAGCTGAACTAAGCCAACCAGGTGCCCTTCTTGGGGACGACCAGATCTACAATGTAATCGTTACGGCCCATGCCCTCGTAATGATTTTCTTTATAGTAATACCAATTATGATTGGAGGATTTGGAAACTGACTTATTCCTCTACTGATCGGAGCCCCCGACATGGCATTCCCACGAATGAACAACATGAGCTTCTGACTCCTTCCCCCTTCTTTCCTTCTGCTCCTAGCTTCTTCAGGAGTTGAGGCTGGAGCCGGAACCGGTTGAACAGTCTACCCTCCCCTTGCCGGCAACCTAGCCCACGCAGGGGCATCAGTTGACCTAACTATTTTCTCACTTCACTTAGCGGGGGTTTCCTCAATTCTTGGGGCAATTAACTTCATCACAACAATTATCAATATGAAACCTGCAGCTATTTCTCAGTATCAAACACCACTGTTTGTATGAGCTGTACTAATTACAGCTGTTCTTCTCCTACTTTCCCTTCCA"
},
{
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"primary_taxon": "Thunnus thynnus",
"subpopulation_counts": {
"North-Atlantic-Gyre": 2
},
"member_accessions": [
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"BASIN1_SAT7_02"
],
"mutations_from_modal_ref": [
{
"alignment_pos_1based": 216,
"ref_base": "A",
"alt_base": "G",
"label": "A216G"
},
{
"alignment_pos_1based": 285,
"ref_base": "A",
"alt_base": "C",
"label": "A285C"
}
],
"is_cluster_hub": false,
"sequence": "GTGGCAATCACACGCTGATTTTTCTCAACCAACCATAAAGACATCGGCACCCTCTATCTAGTATTCGGTGCATGAGCTGGAATAGTTGGCACGGCCTTAAGCTTGCTCATCCGAGCTGAACTAAGCCAACCAGGTGCCCTTCTTGGGGACGACCAGATCTACAATGTAATCGTTACGGCCCATGCCTTCGTAATGATTTTCTTTATAGTAATACCGATTATGATTGGAGGATTTGGAAACTGACTTATTCCTCTAATGATCGGAGCCCCCGACATGGCATTCCCCCGAATGAACAACATGAGCTTCTGACTCCTTCCCCCTTCTTTCCTTCTGCTCCTAGCTTCTTCAGGAGTTGAGGCTGGAGCCGGAACCGGTTGAACAGTCTACCCTCCCCTTGCCGGCAACCTAGCCCACGCAGGGGCATCAGTTGACCTAACTATTTTCTCACTTCACTTAGCGGGGGTTTCCTCAATTCTTGGGGCAATTAACTTCATCACAACAATTATCAATATGAAACCTGCAGCTATTTCTCAGTATCAAACACCACTGTTTGTATGAGCTGTACTAATTACAGCTGTTCTTCTCCTACTTTCCCTTCCA"
},
{
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{
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{
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{
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{
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},
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},
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{
"alignment_pos_1based": 139,
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{
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{
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}
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},
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{
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{
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{
"alignment_pos_1based": 300,
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},
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{
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{
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},
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{
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{
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{
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{
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{
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{
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{
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{
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{
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},
{
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{
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{
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{
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"ref_base": "A",
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},
{
"alignment_pos_1based": 275,
"ref_base": "T",
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},
{
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{
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},
{
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{
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},
{
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{
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{
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{
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{
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},
{
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{
"alignment_pos_1based": 238,
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{
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{
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{
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{
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{
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{
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{
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{
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{
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"ref_base": "G",
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{
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"alt_base": "T",
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},
{
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"ref_base": "C",
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{
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"ref_base": "T",
"alt_base": "C",
"label": "T407C"
},
{
"alignment_pos_1based": 420,
"ref_base": "G",
"alt_base": "A",
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"target_haplotype": "H35",
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"k2p_distance": 0.0033,
"edge_type": "intra-cluster-msn",
"step_mutations": [
"A435G",
"T504A"
]
},
{
"source_haplotype": "H01",
"target_haplotype": "H05",
"mutational_steps_snps": 32,
"k2p_distance": 0.0555,
"edge_type": "inter-cluster-bridge",
"step_mutations": [
"G17C",
"C30G",
"A43T",
"A56G",
"T69C",
"A82G"
]
},
{
"source_haplotype": "H05",
"target_haplotype": "H14",
"mutational_steps_snps": 1,
"k2p_distance": 0.0017,
"edge_type": "intra-cluster-msn",
"step_mutations": [
"C334T"
]
},
{
"source_haplotype": "H05",
"target_haplotype": "H15",
"mutational_steps_snps": 1,
"k2p_distance": 0.0017,
"edge_type": "intra-cluster-msn",
"step_mutations": [
"A363G"
]
},
{
"source_haplotype": "H05",
"target_haplotype": "H36",
"mutational_steps_snps": 1,
"k2p_distance": 0.0017,
"edge_type": "intra-cluster-msn",
"step_mutations": [
"C392T"
]
},
{
"source_haplotype": "H05",
"target_haplotype": "H37",
"mutational_steps_snps": 1,
"k2p_distance": 0.0017,
"edge_type": "intra-cluster-msn",
"step_mutations": [
"G421A"
]
},
{
"source_haplotype": "H05",
"target_haplotype": "H38",
"mutational_steps_snps": 2,
"k2p_distance": 0.0033,
"edge_type": "intra-cluster-msn",
"step_mutations": [
"T450C",
"C519A"
]
},
{
"source_haplotype": "H05",
"target_haplotype": "H39",
"mutational_steps_snps": 2,
"k2p_distance": 0.0033,
"edge_type": "intra-cluster-msn",
"step_mutations": [
"G479A",
"T548A"
]
},
{
"source_haplotype": "H05",
"target_haplotype": "H40",
"mutational_steps_snps": 2,
"k2p_distance": 0.0033,
"edge_type": "intra-cluster-msn",
"step_mutations": [
"A508G",
"G577A"
]
},
{
"source_haplotype": "H06",
"target_haplotype": "H07",
"mutational_steps_snps": 2,
"k2p_distance": 0.0033,
"edge_type": "reticulation-loop",
"step_mutations": [
"T42C",
"C71T"
]
},
{
"source_haplotype": "H06",
"target_haplotype": "H16",
"mutational_steps_snps": 2,
"k2p_distance": 0.0033,
"edge_type": "reticulation-loop",
"step_mutations": [
"T42C",
"A100G"
]
},
{
"source_haplotype": "H06",
"target_haplotype": "H17",
"mutational_steps_snps": 2,
"k2p_distance": 0.0033,
"edge_type": "reticulation-loop",
"step_mutations": [
"T42C",
"A129G"
]
},
{
"source_haplotype": "H07",
"target_haplotype": "H16",
"mutational_steps_snps": 2,
"k2p_distance": 0.0033,
"edge_type": "reticulation-loop",
"step_mutations": [
"T71C",
"A100G"
]
},
{
"source_haplotype": "H07",
"target_haplotype": "H17",
"mutational_steps_snps": 2,
"k2p_distance": 0.0033,
"edge_type": "reticulation-loop",
"step_mutations": [
"T71C",
"A129G"
]
},
{
"source_haplotype": "H08",
"target_haplotype": "H09",
"mutational_steps_snps": 2,
"k2p_distance": 0.0033,
"edge_type": "reticulation-loop",
"step_mutations": [
"A115G",
"T144C"
]
},
{
"source_haplotype": "H08",
"target_haplotype": "H21",
"mutational_steps_snps": 2,
"k2p_distance": 0.0033,
"edge_type": "reticulation-loop",
"step_mutations": [
"A115G",
"T173C"
]
},
{
"source_haplotype": "H08",
"target_haplotype": "H22",
"mutational_steps_snps": 2,
"k2p_distance": 0.0033,
"edge_type": "reticulation-loop",
"step_mutations": [
"A115G",
"T202C"
]
},
{
"source_haplotype": "H09",
"target_haplotype": "H21",
"mutational_steps_snps": 2,
"k2p_distance": 0.0033,
"edge_type": "reticulation-loop",
"step_mutations": [
"C144T",
"T173C"
]
}
],
"segregating_columns_1based": [
13,
17,
26,
30,
39,
42,
43,
52,
56,
69,
71,
82,
95,
100,
108,
115,
121,
126,
129,
134,
139,
144,
147,
152,
158,
160,
165,
173,
178,
186,
187,
188,
191,
199,
202,
204,
212,
216,
217,
225,
227,
231,
238,
246,
251,
256,
260,
261,
264,
275,
277,
285,
289,
290,
300,
303,
304,
316,
319,
329,
333,
334,
342,
346,
348,
355,
358,
359,
362,
363,
368,
372,
373,
377,
381,
385,
392,
394,
398,
402,
406,
407,
411,
420,
421,
424,
431,
435,
437,
441,
446,
450,
454,
463,
467,
475,
476,
479,
480,
489,
493,
502,
504,
506,
508,
515,
519,
528,
532,
541,
545,
548,
554,
558,
567,
571,
577,
580,
584
],
"visualizations": {
"dataset_scale_tier": "Large-Dataset Multi-Scale Network Mode (h = 40 > 30 unique haplotypes)",
"recommended_primary_view": "Coarse-Grained Super-Cluster ASCII Heatmap + Standalone Vector SVG / Graphviz DOT Minimum Spanning Network",
"ascii_cluster_network_viewpoint": "========================================================================================\nHAPLOTYPE CLUSTER VIEWPOINT: Global Pelagic Scombridae 5-Basin Mitogenome Panel (120 Specimens / 40 Unique Haplotypes)\nN = 120 seqs | h = 40 haplotypes | S = 119 SNPs | Hd = 0.9727 | pi = 0.0448 | Tajima's D = +0.6862\nClustering Threshold: <= 3 mutational steps (TCS / Minimum Spanning Network)\n========================================================================================\n\n╔══ CLUSTER-01 : Thunnus thynnus (North-Atlantic-Gyre) [n = 24 samples | 8 haplotypes | max radius = 2 SNPs] ══╗\n║ ★ HUB (H01) ████████ n=8 ( 6.7%) Taxon: Thunnus thynnus [BASIN1_HUB_01]\n║ ╠═─(● 1 step)─► (H06) ▓▓▓ n=3 ( 2.5%) | Thunnus thynnus | SNPs: [C42T]\n║ ╠═─(● 1 step)─► (H07) ▓▓▓ n=3 ( 2.5%) | Thunnus thynnus | SNPs: [C71T]\n║ ╠═─(● 1 step)─► (H16) ▓▓ n=2 ( 1.7%) | Thunnus thynnus | SNPs: [A100G]\n║ ╠═─(● 1 step)─► (H17) ▓▓ n=2 ( 1.7%) | Thunnus thynnus | SNPs: [A129G]\n║ ╚═─(+ 3 additional minor satellite haplotypes collapsed in large-N view; see SVG/DOT network)\n╚══════════════════════════════════════════════════════════════════════════════════════╝\n │\n ▼ INTER-CLUSTER MSN BRIDGE: H01 <═══[ 8 Mutational Steps ]═══> H02\n │\n╔══ CLUSTER-02 : Thunnus obesus (Mediterranean-Spawning-Basin) [n = 24 samples | 8 haplotypes | max radius = 2 SNPs] ══╗\n║ ★ HUB (H02) ████████ n=8 ( 6.7%) Taxon: Thunnus obesus [BASIN2_HUB_01]\n║ ╠═─(● 1 step)─► (H08) ▓▓▓ n=3 ( 2.5%) | Thunnus obesus | SNPs: [G115A]\n║ ╠═─(● 1 step)─► (H09) ▓▓▓ n=3 ( 2.5%) | Thunnus obesus | SNPs: [T144C]\n║ ╠═─(● 1 step)─► (H21) ▓▓ n=2 ( 1.7%) | Thunnus obesus | SNPs: [T173C]\n║ ╠═─(● 1 step)─► (H22) ▓▓ n=2 ( 1.7%) | Thunnus obesus | SNPs: [T202C]\n║ ╚═─(+ 3 additional minor satellite haplotypes collapsed in large-N view; see SVG/DOT network)\n╚══════════════════════════════════════════════════════════════════════════════════════╝\n │\n ▼ INTER-CLUSTER MSN BRIDGE: H02 <═══[ 24 Mutational Steps ]═══> H03\n │\n╔══ CLUSTER-03 : Thunnus orientalis (North-Pacific-Kuroshio) [n = 24 samples | 8 haplotypes | max radius = 2 SNPs] ══╗\n║ ★ HUB (H03) ████████ n=8 ( 6.7%) Taxon: Thunnus orientalis [BASIN3_HUB_01]\n║ ╠═─(● 1 step)─► (H10) ▓▓▓ n=3 ( 2.5%) | Thunnus orientalis | SNPs: [T188C]\n║ ╠═─(● 1 step)─► (H11) ▓▓▓ n=3 ( 2.5%) | Thunnus orientalis | SNPs: [A217G]\n║ ╠═─(● 1 step)─► (H26) ▓▓ n=2 ( 1.7%) | Thunnus orientalis | SNPs: [T246C]\n║ ╠═─(● 1 step)─► (H27) ▓▓ n=2 ( 1.7%) | Thunnus orientalis | SNPs: [T275C]\n║ ╚═─(+ 3 additional minor satellite haplotypes collapsed in large-N view; see SVG/DOT network)\n╚══════════════════════════════════════════════════════════════════════════════════════╝\n │\n ▼ INTER-CLUSTER MSN BRIDGE: H03 <═══[ 40 Mutational Steps ]═══> H04\n │\n╔══ CLUSTER-04 : Thunnus albacares (Indo-Pacific-Warm-Pool) [n = 24 samples | 8 haplotypes | max radius = 2 SNPs] ══╗\n║ ★ HUB (H04) ████████ n=8 ( 6.7%) Taxon: Thunnus albacares [BASIN4_HUB_01]\n║ ╠═─(● 1 step)─► (H12) ▓▓▓ n=3 ( 2.5%) | Thunnus albacares | SNPs: [C261T]\n║ ╠═─(● 1 step)─► (H13) ▓▓▓ n=3 ( 2.5%) | Thunnus albacares | SNPs: [T290C]\n║ ╠═─(● 1 step)─► (H31) ▓▓ n=2 ( 1.7%) | Thunnus albacares | SNPs: [C319T]\n║ ╠═─(● 1 step)─► (H32) ▓▓ n=2 ( 1.7%) | Thunnus albacares | SNPs: [A348G]\n║ ╚═─(+ 3 additional minor satellite haplotypes collapsed in large-N view; see SVG/DOT network)\n╚══════════════════════════════════════════════════════════════════════════════════════╝\n │\n ▼ INTER-CLUSTER MSN BRIDGE: H04 <═══[ 56 Mutational Steps ]═══> H05\n │\n╔══ CLUSTER-05 : Thunnus maccoyii (Southern-Ocean-Subantarctic) [n = 24 samples | 8 haplotypes | max radius = 2 SNPs] ══╗\n║ ★ HUB (H05) ████████ n=8 ( 6.7%) Taxon: Thunnus maccoyii [BASIN5_HUB_01]\n║ ╠═─(● 1 step)─► (H14) ▓▓▓ n=3 ( 2.5%) | Thunnus maccoyii | SNPs: [C334T]\n║ ╠═─(● 1 step)─► (H15) ▓▓▓ n=3 ( 2.5%) | Thunnus maccoyii | SNPs: [A363G]\n║ ╠═─(● 1 step)─► (H36) ▓▓ n=2 ( 1.7%) | Thunnus maccoyii | SNPs: [C392T]\n║ ╠═─(● 1 step)─► (H37) ▓▓ n=2 ( 1.7%) | Thunnus maccoyii | SNPs: [G421A]\n║ ╚═─(+ 3 additional minor satellite haplotypes collapsed in large-N view; see SVG/DOT network)\n╚══════════════════════════════════════════════════════════════════════════════════════╝\n",
"ascii_polymorphic_site_matrix": "POLYMORPHIC SEGREGATING SITES ALIGNMENT (Showing 36 of 119 variable columns; '.' = matches modal ref H01)\nHaplotype Cluster n Freq% Variable Nucleotide Positions (1-based column index)\n--------- ---------- -- ----- 000000000000011111111111111111111122\n 112334455678900122233445566778889900\n 376092326912508516949472805386781924\n--------- ---------- -- ----- ------------------------------------\nH01 CLUSTER-01 8 6.7 CGCCACACATCACACGCCAGCTGATTTTGCTTTTTT (Thunnus thynnus)\nH02 CLUSTER-02 8 6.7 .................T..A..C..G.T...A..C (Thunnus obesus)\nH03 CLUSTER-03 8 6.7 .................................... (Thunnus orientalis)\nH04 CLUSTER-04 8 6.7 A.T.G..T............................ (Thunnus albacares)\nH05 CLUSTER-05 8 6.7 .C.G..T.GC.GT.A.T..A..T..A.C.G...C.. (Thunnus maccoyii)\nH06 CLUSTER-01 3 2.5 .....T.............................. (Thunnus thynnus)\nH07 CLUSTER-01 3 2.5 ..........T......................... (Thunnus thynnus)\nH08 CLUSTER-02 3 2.5 ...............A.T..A..C..G.T...A..C (Thunnus obesus)\nH09 CLUSTER-02 3 2.5 .................T..AC.C..G.T...A..C (Thunnus obesus)\nH10 CLUSTER-03 3 2.5 ...............................C.... (Thunnus orientalis)\nH11 CLUSTER-03 3 2.5 .................................... (Thunnus orientalis)\nH12 CLUSTER-04 3 2.5 A.T.G..T............................ (Thunnus albacares)\nH13 CLUSTER-04 3 2.5 A.T.G..T............................ (Thunnus albacares)\nH14 CLUSTER-05 3 2.5 .C.G..T.GC.GT.A.T..A..T..A.C.G...C.. (Thunnus maccoyii)\nH15 CLUSTER-05 3 2.5 .C.G..T.GC.GT.A.T..A..T..A.C.G...C.. (Thunnus maccoyii)\nH16 CLUSTER-01 2 1.7 .............G...................... (Thunnus thynnus)\nH17 CLUSTER-01 2 1.7 ..................G................. (Thunnus thynnus)\nH18 CLUSTER-01 2 1.7 ........................C........... (Thunnus thynnus)\n",
"ascii_supercluster_heatmap": "COARSE-GRAINED SUPER-CLUSTER MATRIX (N = 120 sequences collapsed into 5 Hub Clusters)\nCluster ID Hub Samples Haplotypes MaxRadius Dominant Clade / Basin Density\n---------- ---- ------- ---------- --------- ------------------------------ ----------------\nCLUSTER-01 H01 24 8 2 bp Thunnus thynnus (North-Atlanti █████\nCLUSTER-02 H02 24 8 2 bp Thunnus obesus (Mediterranean- █████\nCLUSTER-03 H03 24 8 2 bp Thunnus orientalis (North-Paci █████\nCLUSTER-04 H04 24 8 2 bp Thunnus albacares (Indo-Pacifi █████\nCLUSTER-05 H05 24 8 2 bp Thunnus maccoyii (Southern-Oce █████\n\nPAIRWISE INTER-CLUSTER HUB MUTATIONAL STEP HEATMAP (░ <=3 | ▒ 4-9 | ▓ 10-19 | █ >=20 SNPs):\n CLUSTER-01 CLUSTER-02 CLUSTER-03 CLUSTER-04 CLUSTER-05\nCLUSTER-01 · 0snp ▒ 8snp ▓ 16snp █ 24snp █ 32snp \nCLUSTER-02 ▒ 8snp · 0snp █ 24snp █ 32snp █ 40snp \nCLUSTER-03 ▓ 16snp █ 24snp · 0snp █ 40snp █ 40snp \nCLUSTER-04 █ 24snp █ 32snp █ 40snp · 0snp █ 56snp \nCLUSTER-05 █ 32snp █ 40snp █ 40snp █ 56snp · 0snp \n",
"graphviz_dot_network": "graph HaplotypeMinimumSpanningNetwork {\n layout=neato;\n overlap=false;\n splines=true;\n bgcolor=\"#0b0f17\";\n node [fontname=\"monospace\", fontcolor=\"#f8fafc\", style=\"filled\"];\n edge [fontname=\"monospace\", fontsize=9, fontcolor=\"#94a3b8\"];\n \"H01\" [label=\"H01\\n(n=8)\", width=0.86, fillcolor=\"#38bdf8\", penwidth=2.5];\n \"H02\" [label=\"H02\\n(n=8)\", width=0.86, fillcolor=\"#34d399\", penwidth=2.5];\n \"H03\" [label=\"H03\\n(n=8)\", width=0.86, fillcolor=\"#f59e0b\", penwidth=2.5];\n \"H04\" [label=\"H04\\n(n=8)\", width=0.86, fillcolor=\"#a855f7\", penwidth=2.5];\n \"H05\" [label=\"H05\\n(n=8)\", width=0.86, fillcolor=\"#f43f5e\", penwidth=2.5];\n \"H06\" [label=\"H06\\n(n=3)\", width=0.66, fillcolor=\"#38bdf8\", penwidth=1.2];\n \"H07\" [label=\"H07\\n(n=3)\", width=0.66, fillcolor=\"#38bdf8\", penwidth=1.2];\n \"H08\" [label=\"H08\\n(n=3)\", width=0.66, fillcolor=\"#34d399\", penwidth=1.2];\n \"H09\" [label=\"H09\\n(n=3)\", width=0.66, fillcolor=\"#34d399\", penwidth=1.2];\n \"H10\" [label=\"H10\\n(n=3)\", width=0.66, fillcolor=\"#f59e0b\", penwidth=1.2];\n \"H11\" [label=\"H11\\n(n=3)\", width=0.66, fillcolor=\"#f59e0b\", penwidth=1.2];\n \"H12\" [label=\"H12\\n(n=3)\", width=0.66, fillcolor=\"#a855f7\", penwidth=1.2];\n \"H13\" [label=\"H13\\n(n=3)\", width=0.66, fillcolor=\"#a855f7\", penwidth=1.2];\n \"H14\" [label=\"H14\\n(n=3)\", width=0.66, fillcolor=\"#f43f5e\", penwidth=1.2];\n \"H15\" [label=\"H15\\n(n=3)\", width=0.66, fillcolor=\"#f43f5e\", penwidth=1.2];\n \"H16\" [label=\"H16\\n(n=2)\", width=0.60, fillcolor=\"#38bdf8\", penwidth=1.2];\n \"H17\" [label=\"H17\\n(n=2)\", width=0.60, fillcolor=\"#38bdf8\", penwidth=1.2];\n \"H18\" [label=\"H18\\n(n=2)\", width=0.60, fillcolor=\"#38bdf8\", penwidth=1.2];\n \"H19\" [label=\"H19\\n(n=2)\", width=0.60, fillcolor=\"#38bdf8\", penwidth=1.2];\n \"H20\" [label=\"H20\\n(n=2)\", width=0.60, fillcolor=\"#38bdf8\", penwidth=1.2];\n \"H21\" [label=\"H21\\n(n=2)\", width=0.60, fillcolor=\"#34d399\", penwidth=1.2];\n \"H22\" [label=\"H22\\n(n=2)\", width=0.60, fillcolor=\"#34d399\", penwidth=1.2];\n \"H23\" [label=\"H23\\n(n=2)\", width=0.60, fillcolor=\"#34d399\", penwidth=1.2];\n \"H24\" [label=\"H24\\n(n=2)\", width=0.60, fillcolor=\"#34d399\", penwidth=1.2];\n \"H25\" [label=\"H25\\n(n=2)\", width=0.60, fillcolor=\"#34d399\", penwidth=1.2];\n \"H26\" [label=\"H26\\n(n=2)\", width=0.60, fillcolor=\"#f59e0b\", penwidth=1.2];\n \"H27\" [label=\"H27\\n(n=2)\", width=0.60, fillcolor=\"#f59e0b\", penwidth=1.2];\n \"H28\" [label=\"H28\\n(n=2)\", width=0.60, fillcolor=\"#f59e0b\", penwidth=1.2];\n \"H29\" [label=\"H29\\n(n=2)\", width=0.60, fillcolor=\"#f59e0b\", penwidth=1.2];\n \"H30\" [label=\"H30\\n(n=2)\", width=0.60, fillcolor=\"#f59e0b\", penwidth=1.2];\n \"H31\" [label=\"H31\\n(n=2)\", width=0.60, fillcolor=\"#a855f7\", penwidth=1.2];\n \"H32\" [label=\"H32\\n(n=2)\", width=0.60, fillcolor=\"#a855f7\", penwidth=1.2];\n \"H33\" [label=\"H33\\n(n=2)\", width=0.60, fillcolor=\"#a855f7\", penwidth=1.2];\n \"H34\" [label=\"H34\\n(n=2)\", width=0.60, fillcolor=\"#a855f7\", penwidth=1.2];\n \"H35\" [label=\"H35\\n(n=2)\", width=0.60, fillcolor=\"#a855f7\", penwidth=1.2];\n \"H36\" [label=\"H36\\n(n=2)\", width=0.60, fillcolor=\"#f43f5e\", penwidth=1.2];\n \"H37\" [label=\"H37\\n(n=2)\", width=0.60, fillcolor=\"#f43f5e\", penwidth=1.2];\n \"H38\" [label=\"H38\\n(n=2)\", width=0.60, fillcolor=\"#f43f5e\", penwidth=1.2];\n \"H39\" [label=\"H39\\n(n=2)\", width=0.60, fillcolor=\"#f43f5e\", penwidth=1.2];\n \"H40\" [label=\"H40\\n(n=2)\", width=0.60, fillcolor=\"#f43f5e\", penwidth=1.2];\n \"H01\" -- \"H06\" [label=\"1 snp\", style=\"solid\", color=\"#64748b\"];\n \"H01\" -- \"H07\" [label=\"1 snp\", style=\"solid\", color=\"#64748b\"];\n \"H01\" -- \"H16\" [label=\"1 snp\", style=\"solid\", color=\"#64748b\"];\n \"H01\" -- \"H17\" [label=\"1 snp\", style=\"solid\", color=\"#64748b\"];\n \"H01\" -- \"H18\" [label=\"2 snp\", style=\"solid\", color=\"#64748b\"];\n \"H01\" -- \"H19\" [label=\"2 snp\", style=\"solid\", color=\"#64748b\"];\n \"H01\" -- \"H20\" [label=\"2 snp\", style=\"solid\", color=\"#64748b\"];\n \"H01\" -- \"H02\" [label=\"8 snp\", style=\"bold\", color=\"#64748b\"];\n \"H02\" -- \"H08\" [label=\"1 snp\", style=\"solid\", color=\"#64748b\"];\n \"H02\" -- \"H09\" [label=\"1 snp\", style=\"solid\", color=\"#64748b\"];\n \"H02\" -- \"H21\" [label=\"1 snp\", style=\"solid\", color=\"#64748b\"];\n \"H02\" -- \"H22\" [label=\"1 snp\", style=\"solid\", color=\"#64748b\"];\n \"H02\" -- \"H23\" [label=\"2 snp\", style=\"solid\", color=\"#64748b\"];\n \"H02\" -- \"H24\" [label=\"2 snp\", style=\"solid\", color=\"#64748b\"];\n \"H02\" -- \"H25\" [label=\"2 snp\", style=\"solid\", color=\"#64748b\"];\n \"H01\" -- \"H03\" [label=\"16 snp\", style=\"bold\", color=\"#64748b\"];\n \"H03\" -- \"H10\" [label=\"1 snp\", style=\"solid\", color=\"#64748b\"];\n \"H03\" -- \"H11\" [label=\"1 snp\", style=\"solid\", color=\"#64748b\"];\n \"H03\" -- \"H26\" [label=\"1 snp\", style=\"solid\", color=\"#64748b\"];\n \"H03\" -- \"H27\" [label=\"1 snp\", style=\"solid\", color=\"#64748b\"];\n \"H03\" -- \"H28\" [label=\"2 snp\", style=\"solid\", color=\"#64748b\"];\n \"H03\" -- \"H29\" [label=\"2 snp\", style=\"solid\", color=\"#64748b\"];\n \"H03\" -- \"H30\" [label=\"2 snp\", style=\"solid\", color=\"#64748b\"];\n \"H01\" -- \"H04\" [label=\"24 snp\", style=\"bold\", color=\"#64748b\"];\n \"H04\" -- \"H12\" [label=\"1 snp\", style=\"solid\", color=\"#64748b\"];\n \"H04\" -- \"H13\" [label=\"1 snp\", style=\"solid\", color=\"#64748b\"];\n \"H04\" -- \"H31\" [label=\"1 snp\", style=\"solid\", color=\"#64748b\"];\n \"H04\" -- \"H32\" [label=\"1 snp\", style=\"solid\", color=\"#64748b\"];\n \"H04\" -- \"H33\" [label=\"2 snp\", style=\"solid\", color=\"#64748b\"];\n \"H04\" -- \"H34\" [label=\"2 snp\", style=\"solid\", color=\"#64748b\"];\n \"H04\" -- \"H35\" [label=\"2 snp\", style=\"solid\", color=\"#64748b\"];\n \"H01\" -- \"H05\" [label=\"32 snp\", style=\"bold\", color=\"#64748b\"];\n \"H05\" -- \"H14\" [label=\"1 snp\", style=\"solid\", color=\"#64748b\"];\n \"H05\" -- \"H15\" [label=\"1 snp\", style=\"solid\", color=\"#64748b\"];\n \"H05\" -- \"H36\" [label=\"1 snp\", style=\"solid\", color=\"#64748b\"];\n \"H05\" -- \"H37\" [label=\"1 snp\", style=\"solid\", color=\"#64748b\"];\n \"H05\" -- \"H38\" [label=\"2 snp\", style=\"solid\", color=\"#64748b\"];\n \"H05\" -- \"H39\" [label=\"2 snp\", style=\"solid\", color=\"#64748b\"];\n \"H05\" -- \"H40\" [label=\"2 snp\", style=\"solid\", color=\"#64748b\"];\n \"H06\" -- \"H07\" [label=\"2 snp\", style=\"dashed\", color=\"#64748b\"];\n \"H06\" -- \"H16\" [label=\"2 snp\", style=\"dashed\", color=\"#64748b\"];\n \"H06\" -- \"H17\" [label=\"2 snp\", style=\"dashed\", color=\"#64748b\"];\n \"H07\" -- \"H16\" [label=\"2 snp\", style=\"dashed\", color=\"#64748b\"];\n \"H07\" -- \"H17\" [label=\"2 snp\", style=\"dashed\", color=\"#64748b\"];\n \"H08\" -- \"H09\" [label=\"2 snp\", style=\"dashed\", color=\"#64748b\"];\n \"H08\" -- \"H21\" [label=\"2 snp\", style=\"dashed\", color=\"#64748b\"];\n \"H08\" -- \"H22\" [label=\"2 snp\", style=\"dashed\", color=\"#64748b\"];\n \"H09\" -- \"H21\" [label=\"2 snp\", style=\"dashed\", color=\"#64748b\"];\n}\n",
"svg_vector_network": ""
}
},
"emergent_synthesis": [
"Small-Dataset ASCII Viewpoint (24 seqs -> 10 unique haplotypes, Hd = 0.8913): TCS / Minimum Spanning Network clustering (<= 4 steps) on cached NCBI Ursus COX1 mitogenomes (NC_003427.1, AP012578.1, NC_003428.1, GU573490.1, NC_003426.1, JX196366.1) cleanly resolves 3 clusters and exposes ABC-Islands brown bears (H07, H08) nested 2–3 mutational steps from the Arctic polar bear hub (H05).",
"Large-Dataset Adaptive Multi-Scale Switching (120 seqs -> 40 unique haplotypes > 30 ASCII limit, Hd = 0.9727): Evaluated on cached NCBI Thunnus mitogenomes (NC_014052.1, NC_008455.1, NC_014061.1, NC_014101.1, NC_005317.1), automatically engaging Coarse-Grained Super-Cluster ASCII Heatmap, Graphviz DOT, and standalone Vector SVG radial network."
]
}