Denisova3

FASTA

Metadata

Reference

Data

identifier	Denisova3
alternative_identifiers	['Denisova', 'X Woman']
country	Russia
continent	Asia
region	Altai
culture	Hunter-Gatherer
epoch	Upper Paleolithic
group	HGE
comment	Denisovan hominin, mix of Upper and Middle Paleolithic features, and Mousterian and Levallois industry
latitude	51.397396087646484
longitude	84.67649841308594
sex	F
site	Denisova cave
site_detail	-
mt_hg	L
ychr_hg	-
year_from	-48000
year_to	-30000
date_detail	40022-39571 calBC (SOAN-2504 using OxCal4.3 (IntCal 13 curve), KIA-25285 (48650±2380), AA-35321 (29200±360))
bp	37235±0
c14_lab_code	SOAN-2504
c14_sample_tag	-
c14_layer_tag	True
avg_coverage	-
sequence_source	bam
reference	Krause et al. 2010. The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature, 464(7290), 894-897. (link)
data_link	https://www.ebi.ac.uk/ena/data/view/FN673705
ychr_snps	-
mitopathos	[{'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': '12311C', 'position': 12311, 'status': 'Reported', 'homoplasmy': '+', 'heteroplasmy': '+', 'locus': ['MT-TL2'], 'diseases': ['CPEO']}, {'allele': '12372A', 'position': 12372, 'status': 'Reported', 'homoplasmy': '+', 'heteroplasmy': '-', 'locus': ['MT-ND5'], 'diseases': ['Altered brain pH / sCJD patients']}, {'allele': '12477C', 'position': 12477, 'status': 'Reported', 'homoplasmy': '+', 'heteroplasmy': '-', 'locus': ['MT-ND5'], 'diseases': ['possible HCM susceptibility']}, {'allele': '12705T', 'position': 12705, 'status': 'Reported', 'homoplasmy': '<NA>', 'heteroplasmy': '<NA>', 'locus': ['MT-CO1'], 'diseases': ['Possible protective factor for normal tension glaucoma']}, {'allele': '13276G', 'position': 13276, 'status': 'Conflicting reports', 'homoplasmy': '+', 'heteroplasmy': '-', 'locus': ['MT-ND5'], 'diseases': ['MIDD+retinopathy']}, {'allele': '13528G', 'position': 13528, 'status': 'Reported', 'homoplasmy': '+', 'heteroplasmy': '-', 'locus': ['MT-ND5'], 'diseases': ['LHON-like / LHON / MELAS']}, {'allele': '14693G', 'position': 14693, 'status': 'Reported', 'homoplasmy': '+', 'heteroplasmy': '+', 'locus': ['MT-TE'], 'diseases': ['MELAS / LHON / DEAF / hypertension helper']}, {'allele': '15043A', 'position': 15043, 'status': 'Reported', 'homoplasmy': '+', 'heteroplasmy': '-', 'locus': ['MT-CYB'], 'diseases': ['MDD-associated']}, {'allele': '150T', 'position': 150, 'status': 'Conflicting reports', 'homoplasmy': '+', 'heteroplasmy': '+', 'locus': ['MT-CR'], 'diseases': ['Longevity / Cervical Carcinoma / HPV infection risk']}, {'allele': '16081G', 'position': 16081, 'status': 'Reported', 'homoplasmy': '-', 'heteroplasmy': '+', 'locus': ['MT-CR'], 'diseases': ['Cyclic Vomiting Syndrome']}, {'allele': '16129A', 'position': 16129, 'status': 'Reported', 'homoplasmy': '-', 'heteroplasmy': '+', 'locus': ['MT-CR'], 'diseases': ['Cyclic Vomiting Syndrome with Migraine']}, {'allele': '310C', 'position': 310, 'status': 'Reported', 'homoplasmy': '<NA>', 'heteroplasmy': '<NA>', 'locus': ['MT-CR'], 'diseases': ['Possible protective factor for normal tension glaucoma']}, {'allele': '3277A', 'position': 3277, 'status': 'Reported', 'homoplasmy': '+', 'heteroplasmy': '-', 'locus': ['MT-TL1'], 'diseases': ['Poss. hypertension factor']}, {'allele': '3290C', 'position': 3290, 'status': 'Reported', 'homoplasmy': '+', 'heteroplasmy': '-', 'locus': ['MT-TL1'], 'diseases': ['Poss. hypertension factor']}, {'allele': '3421A', 'position': 3421, 'status': 'Reported', 'homoplasmy': '+', 'heteroplasmy': '-', 'locus': ['MT-ND1'], 'diseases': ['MIDD']}, {'allele': '3496T', 'position': 3496, 'status': 'Reported / Secondary', 'homoplasmy': '+', 'heteroplasmy': '-', 'locus': ['MT-ND1'], 'diseases': ['LHON']}, {'allele': '4456T', 'position': 4456, 'status': 'Reported', 'homoplasmy': '-', 'heteroplasmy': '+', 'locus': ['MT-TM'], 'diseases': ['Poss. hypertension factor']}, {'allele': '4659A', 'position': 4659, 'status': 'Reported', 'homoplasmy': '+', 'heteroplasmy': '-', 'locus': ['MT-ND2'], 'diseases': ['possible PD risk factor / LHON']}, {'allele': '5821A', 'position': 5821, 'status': 'Reported', 'homoplasmy': '+', 'heteroplasmy': '-', 'locus': ['MT-TC'], 'diseases': ['DEAF helper mut.']}, {'allele': '6150A', 'position': 6150, 'status': 'Reported', 'homoplasmy': '+', 'heteroplasmy': '-', 'locus': ['MT-CO1'], 'diseases': ['Prostate Cancer / enriched in POAG cohort']}, {'allele': '7868T', 'position': 7868, 'status': 'Possibly synergistic', 'homoplasmy': '+', 'heteroplasmy': '-', 'locus': ['MT-CO2'], 'diseases': ['LHON']}, {'allele': '827G', 'position': 827, 'status': 'Conflicting reports', 'homoplasmy': '+', 'heteroplasmy': '-', 'locus': ['MT-RNR1'], 'diseases': ['DEAF']}, {'allele': '8021G', 'position': 8021, 'status': 'Reported', 'homoplasmy': '+', 'heteroplasmy': '-', 'locus': ['MT-CO2'], 'diseases': ['Asthenozoospermia']}, {'allele': '9966A', 'position': 9966, 'status': 'Reported', 'homoplasmy': 'nr', 'heteroplasmy': 'nr', 'locus': ['MT-CO3'], 'diseases': ['LHON possible helper variant']}]