I0744

FASTA

Metadata

Reference

Data

identifier	I0744
alternative_identifiers	['M10-275']
country	Turkey
continent	Asia
region	Anatolia
culture	Anatolia_Neolithic
epoch	Neolithic
group	NENE
comment	-
latitude	40.29999923706055
longitude	29.56999969482422
sex	M
site	Barcın, Marmara Region, Northwest Anatolia
site_detail	-
mt_hg	J1c11
ychr_hg	G2a2b2a
year_from	-6500
year_to	-6200
date_detail	6500-6200 BCE
bp	-
c14_lab_code	-
c14_sample_tag	-
c14_layer_tag	-
avg_coverage	-
sequence_source	bam
reference	Mathieson et al. 2015. Genome-wide patterns of selection in 230 ancient Eurasians. Nature, 528(7583), 499-503. (link)
data_link	https://www.ebi.ac.uk/ena/data/view/PRJEB11450
ychr_snps	['G2a2b2a:CTS688:6953417T->C', 'G2a2b2a:CTS4454^:15655268C->T', 'G2a2b2a:CTS10366:19423576G->A', 'G2a2b2a:P303:21645348T->C', 'G2a2b2a:PF3329:8478026C->A', 'G2a2b2a:PF3342:21935606G->T', 'G2a2b2a:Z3243:21935550A->G', 'G2a2b2:CTS9957:19170699C->T', 'G2a2b:CTS9763:19060222T->G', 'G2a2b:CTS11324:23071312A->T', 'G2a2b:F1733:14229971C->A', 'G2a2b:F2535:17589788C->T', 'G2a2b:F3139:21151007T->C', 'G2a2b:L32:14692227T->C', 'G2a2b:L190:18759690C->T', 'G2a2b:Z3260:13671506G->T', 'G2a2:CTS4367:15615340C->G', 'G2a:CTS6630:17022002C->T', 'G2a:F2274:16802506G->T', 'G2a:F2529:17571517A->G', 'G2a:F3088:20813445G->A', 'G2a:F4086:7727677C->T', 'G2a:L31:14028148C->A', 'G2a:M3393:21493984G->T', 'G2a:M3397:21605685G->C', 'G2a:M3408:22109159G->C', 'G2a:P15:23244026C->T', 'G2a:PF3141:23973594T->G', 'G2:CTS1900:14116322T->A', 'G2:CTS2406:14294068C->T', 'G2:CTS4703:15776024C->Thet', 'G2:CTS7662:17597715C->T', 'G2:CTS10089:19248446G->A', 'G2:F1239:8482393C->T', 'G2:F1294:8545324T->A', 'G2:F1393:8719593G->A', 'G2:F3070:19493301A->G', 'G2:F3198:21401188G->T', 'G2:F3220:21637589G->C', 'G2:F3344:22697266G->A', 'G2:F3536:23768744C->T', 'G2:L89:7978725C->T', 'G2:M3446:6685638A->C', 'G2:M3579:21147058A->G', 'G2:P287:22072097G->T', 'G:CTS34:2681740G->A', 'G:CTS175:2785630A->T', 'G:CTS692:6955839A->G', 'G:CTS1013:7145960C->T', 'G:CTS1283:7309873T->G', 'G:CTS2251:14235140C->T', 'G:CTS2271:14243137C->T', 'G:CTS2357:14273557C->T', 'G:CTS2506:14333087C->A', 'G:CTS4238:15504804C->T', 'G:CTS4761:15802681C->T', 'G:CTS4887:15888550C->T', 'G:CTS5699:16439267G->A', 'G:CTS6957:17210745C->T', 'G:CTS7092:17281783G->A', 'G:CTS7269:17393643T->C', 'G:CTS7674:17610571G->A', 'G:CTS8023:17798903T->C', 'G:CTS8531:18070349G->C', 'G:CTS9011:18615020A->T', 'G:CTS9593:18979775T->A', 'G:CTS9641:19010380G->A', 'G:CTS10026:19215139A->T', 'G:CTS10723:22730922C->G', 'G:CTS10945:22848965A->G', 'G:CTS11185:22997377C->G', 'G:CTS11228:23023554C->A', 'G:CTS11331:23074190A->G', 'G:CTS11529:23151673T->C', 'G:CTS11911:23346582A->C', 'G:CTS13035:28783924C->A', 'G:F1131:8240725C->T', 'G:F1383:8700380C->T', 'G:F1551:9448354A->G', 'G:F2076:16185081A->G', 'G:F2906:18957208C->T', 'G:L116:14989721C->G', 'G:L382:14469411C->A', 'G:L522:17533325A->C', 'G:L770:2863466A->T', 'G:L837:17853245A->G', 'G:M3258:7992031T->C', 'G:M3432:23578115C->G', 'G:M3450:6931141C->G', 'G:M3468:7744050T->C', 'G:M3472:7899682T->C', 'G:M3473:7927218C->T', 'G:M3474:7930724C->A', 'G:M3479:8231862G->C', 'G:M3480:8327892T->A', 'G:M3482:8454233G->A', 'G:M3485:8563874C->T', 'G:M3486:8600158A->T', 'G:M3489:8691654G->C', 'G:M3593:21648433C->G', 'G:M3597:21865624G->A', 'G:M3599:21939157G->A', 'G:M3604:22167631C->T', 'G:M3605:22170577T->G', 'G:M3609:22651339C->T', 'G:M3628:23793740C->A', 'G:P257:14432928G->A', 'G:PF2918:13679469G->A', 'G:PF2920:13824120T->G', 'G:PF2952:14577177G->A', 'G:PF3045:20823823C->T', 'G:PF3134:15275200C->G', 'G:S1435:13658486C->Ghet', 'G:U21:15204710A->C', 'G:Z3262:13676268G->A', 'G:Z6325:13806058C->T']
mitopathos	[{'allele': '11251G', 'position': 11251, 'status': 'Reported', 'homoplasmy': 'nr', 'heteroplasmy': 'nr', 'locus': ['MT-ND4'], 'diseases': ['Reduced risk of PD']}, {'allele': '10398G', 'position': 10398, 'status': 'Reported / lineage L & M marker / also hg IJK', 'homoplasmy': '+', 'heteroplasmy': '-', 'locus': ['MT-ND3'], 'diseases': ['PD protective factor / longevity / altered cell pH / metabolic syndrome / breast cancer risk / Leigh Syndrome risk / ADHD / cognitive decline / SCA2 age of onset / Fuchs endothelial corneal dystrophy']}, {'allele': '13708A', 'position': 13708, 'status': 'Conflicting reports', 'homoplasmy': '+', 'heteroplasmy': '+', 'locus': ['MT-ND5'], 'diseases': ['LHON / Increased MS risk / higher freq in PD-ADS']}, {'allele': '185A', 'position': 185, 'status': 'Reported', 'homoplasmy': '+', 'heteroplasmy': '-', 'locus': ['MT-CR'], 'diseases': ['Low VO2max response']}, {'allele': '295T', 'position': 295, 'status': 'Reported', 'homoplasmy': '+', 'heteroplasmy': '-', 'locus': ['MT-CR'], 'diseases': ['Low VO2max response']}, {'allele': '3010A', 'position': 3010, 'status': 'Reported', 'homoplasmy': '+', 'heteroplasmy': '-', 'locus': ['MT-RNR2'], 'diseases': ['Cyclic Vomiting Syndrome with Migraine / high altitude disease risk factor']}, {'allele': '228A', 'position': 228, 'status': 'Reported', 'homoplasmy': '+', 'heteroplasmy': '-', 'locus': ['MT-CR'], 'diseases': ['Low VO2max response']}, {'allele': '4216C', 'position': 4216, 'status': 'Conflicting reports', 'homoplasmy': '+', 'heteroplasmy': '-', 'locus': ['MT-ND1'], 'diseases': ['LHON / Insulin Resistance /possible adaptive high altitude variant / miscarriage']}, {'allele': '462T', 'position': 462, 'status': 'Reported', 'homoplasmy': '+', 'heteroplasmy': '-', 'locus': ['MT-CR'], 'diseases': ['Low VO2max response']}, {'allele': '489C', 'position': 489, 'status': 'Reported', 'homoplasmy': '+', 'heteroplasmy': '-', 'locus': ['MT-CR'], 'diseases': ['Low VO2max response']}]