Schema for Denisova Seq - Denisova High-Coverage Sequence Reads
  Database: hg19    Primary Table: dhcBamDenisova
BAM File: /gbdb/hg19/bbi/T_hg19_1000g.bam
Format description: The fields of a SAM short read alignment, the text version of BAM.
See the SAM Format Specification for more details
fielddescription
qNameQuery template name - name of a read
flagFlags. 0x10 set for reverse complement. See SAM docs for others.
rNameReference sequence name (often a chromosome)
pos1 based position
mapQMapping quality 0-255, 255 is best
cigarCIGAR encoded alignment string.
rNextRef sequence for next (mate) read. '=' if same as rName, '*' if no mate
pNextPosition (1-based) of next (mate) sequence. May be -1 or 0 if no mate
tLenSize of DNA template for mated pairs. -size for one of mate pairs
seqQuery template sequence
qualASCII of Phred-scaled base QUALity+33. Just '*' if no quality scores
tagTypeValsTab-delimited list of tag:type:value optional extra fields

Sample Rows
 
qNameflagrNameposmapQcigarrNextpNexttLenseqqualtagTypeVals
M_SOLEXA-GA03_PEi_JK_3004_5:2:2:4832:19167#GTCGACT1619990372M1I3M1D5M3I105M*00TGCTCTTCCGATCTTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA;96888=;;:<;9;>BD8NXJPWNOXLMTLWUPQ]RV]TWVOYZQQ\R[]STWVVZRY]UUWRVV?S[RWZNUTLUWNQQKSRO<P=OQGJP>KLF>I9IL;<><;:?>>9<9>:=298X0:C:1 X1:C:0 RG:Z:SL3004 XG:C:3 XM:C:4 XN:C:11 XO:C:1 XP:C:1 XT:A:N NM:f:15 MD:Z:0N0N0N0N0N0^N0N0N0N0N0N105
M_SOLEXA-GA03_PEi_JK_3004_5:5:4:12109:5782#GTCGACT16199902599M*00TGCTCTTCCGATCTCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACP&R+IN-OY*&T-&UX[V[VUZ]W[]R]Y&]]Z[]V\[X\]U]]W]\W]VW]XY[]YWYQ\ZQ\U'UVSPKOURJQNCTPLNHIPQ+OLBQMNFK(I@BX0:C:1 X1:C:0 RG:Z:SL3004 XG:C:0 XM:C:6 XN:C:11 XO:C:0 XP:C:1 XT:A:N NM:f:13 MD:Z:0N0N0N0N0N0N0N0N0N0N0N1A0A85
M_SOLEXA-GA04_PEi_JK_3004_3:1:17:10437:15314#GTCGACT161999201S3M1D6M1I104M*00CTCTTCCGATCTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA:<<>A>>=?@=@B=RWTV[OYWVUZQX[[[]XZ\\]\VVYYZ]YXWZ][UVY[][U[XZ][TYWZ\\TXTU]XURUW[VQRURTPORPQTOLOMPSQRNL<B>>?<:@<=<=7?<X0:C:3 X1:C:2 RG:Z:SL3004 XG:C:1 XM:C:5 XN:C:9 XO:C:1 XP:C:1 XT:A:R NM:f:11 MD:Z:0N0N0N0^N0N0N0N0N0N1A103
M_SOLEXA-GA04_PEi_JK_3004_3:3:63:12078:19790#GTCGACT161999201S3M1D6M1I100M*00CTCTTCCGATCTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCINPOWKNITVMV]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]WWNLLHEMHGKX0:C:3 X1:C:2 RG:Z:SL3004 XG:C:1 XM:C:5 XN:C:9 XO:C:1 XP:C:2 XT:A:R NM:f:11 MD:Z:0N0N0N0^N0N0N0N0N0N1A99
M_SOLEXA-GA01_PEi_JK_3003:8:103:11393:9893#GTCGACT1619993379M2D1M1I48M*00CTCTCCGATCTCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACOPQPOMLQUMVJTWYYRPTTZVQQTTUULPN4XZ58PU[YTSQX[VUSUQXSQ5544X3X0:C:1 X1:C:0 RG:Z:SL3003 XG:C:1 XM:C:3 XN:C:8 XO:C:1 XP:C:1 XT:A:U NM:f:11 MD:Z:0N0N0N0N0N0N0N0N1^AA49
M_SOLEXA-GA04_PE_JK_3003_3004:2:77:8600:6548#GTCGACT1619993372M1I69M*00CTCTTCCGATCTCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]X0:C:1 X1:C:0 RG:Z:SL3003 XG:C:1 XM:C:4 XN:C:8 XO:C:1 XP:C:2 XT:A:U NM:f:11 MD:Z:0N0N0N0N0N0N0N0N1A0A60
M_SOLEXA-GA04_PE_JK_3003_3004:8:79:12864:2014#GTCGACT16199962399M*00TCCTATCTCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACN%M&(R%)Q%+U&%VRZTX]PWWXY]QXZXU[VU\XY]UX\WV]W[]Z[]YYYZ]]UW\Z]]UWYWYZWRXSZ[TTUTZZTRTQTSNOPOUONHKCOLFX0:C:1 X1:C:1 XA:Z:12,+95645,99M,4; RG:Z:SL3004 XG:C:0 XM:C:3 XN:C:5 XO:C:0 XP:C:1 XT:A:U NM:f:7 MD:Z:0N0N0N0N0N1A0A91
M_SOLEXA-GA03_00034_PEdi_MM_11:1:118:12822:14441#TGGACGT,NTGAAGT16199972053M*00CCGATCTCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCT]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]X0:C:1 X1:C:2 XA:Z:1,+249240493,53M,3;1,+249240407,53M,3; RG:Z:B1133 XG:C:0 XM:C:2 XN:C:4 XO:C:0 XP:C:2 XT:A:U NM:f:6 MD:Z:0N0N0N0N1A0A46
M_SOLEXA-GA04_00029_PEdi_MM_9:6:11:7346:11551#CGTTGGT,NGCGTCC161999809M1D49M*00TGAATACCCAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA]\]]]]Z]]]][]]Z]]Z]]Z]][]\]]][[]\Z]]][\][]]YZ]]Z]]\][\[ZZ]X0:C:15 X1:C:0 RG:Z:B1130 XG:C:1 XM:C:3 XN:C:3 XO:C:1 XP:C:1 XT:A:R NM:f:6 MD:Z:0N0N0N0T0A4^T49
M_SOLEXA-GA01_PEi_JK_3003:6:120:8148:4801#GTCGACT01999937115M*00GATAAACCTAAGCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTCACCCTAACC45:;:4726<:5878>NCHLFP8HKNMOFJEMNLPNROSQURVRQVS9SOVXNVOWTYVPTNT]RRQSRUXKWRPYSURSOSPQOQPONLVMOMONMNLNF;7;?38768365;2X0:C:1 X1:C:0 RG:Z:SL3003 XG:C:0 XM:C:5 XN:C:2 XO:C:0 XP:C:1 XT:A:U NM:f:7 MD:Z:0N0N3C5C93A4A1C2

Denisova Seq (dhcBamDenisova) Track Description
 
Denisova cave
Denisova cave entrance in the Altai Mountains of Siberia, Russia where the bones were found from which DNA was sequenced (Copyright (C) 2010, Johannes Krause)

Description

The Denisova Sequence track shows high-coverage sequence reads from an archaic Denisovan individual mapped to the human genome reference assembly. The Denisova DNA was extracted from a phalanx bone excavated from Denisova Cave in the Altai Mountains in southern Siberia.

Methods

A novel single-stranded DNA library preparation method (Note 2, supplementary online materials of Meyer, 2012) was applied to DNA previously extracted from 40mg of bone (Reich, 2010). Using single-stranded DNA greatly increased the genomic coverage to 30X compared to an earlier 1.9X sequence (Reich, 2010). Sequence reads were aligned to human sequence Feb. 2009 (GRCh37/hg19) (downloaded from the 1000 Genomes Project) using the Burrows-Wheeler Aligner.

Credits

Thanks to the Max Planck Institute for Evolutionary Anthropology for providing the BAM files used for this track.

References

Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prüfer K, de Filippo C et al. A high-coverage genome sequence from an archaic Denisovan individual. Science. 2012 Oct 12;338(6104):222-6. PMID: 22936568; PMC: PMC3617501; supplementary online materials, Note 2

Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PL et al. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature. 2010 Dec 23;468(7327):1053-60. PMID: 21179161