Hi Claudia, It seems that you used the Table Browser feature with the output set to 'sequence' to obtain sequences of the Neandertal contig and sequence reads you provided in you email. With 'sequence' selected as your output, you are actually obtaining the hg19 assembly sequence at the coordinates of your items. It sounds like what you really want is the sequence of the Neandertal contig or sequence read. To do this, set the table browser output to 'all fields from selected table' and the output you get will have the sequence of the contig or sequence read of interest.
I did this and here are the results from Neandertal Cntgs at chr4:163076838-163076891: #qName flag rName pos mapQ cigar rNext pNext tLen seq qual tagTypeVals Vi33.26-hg18_8275939 0 chr4 163076838 254 54M * 0 0 TTGCTTTCTTTATTCCTACACATATACATAATTTACATAATCTAAGTGTGTGTA +-CA357M999(99MM9(M(M(9(9(M(9((999(M(9((9M9((C9C9=9@9( AS:C:0 Here are the results from Neandertal Seq at chr4:163076838-163076891: #qName flag rName pos mapQ cigar rNext pNext tLen seq qual tagTypeVals C_M_SOLEXA-GA02_JK_PE51_SL29_SL30_SL31_rep:3:87:1372:1837 0 chr4 163076838 204 54M * 0 0 TTGCTTTCTTTATTCCTACACATATACATAATTTACATAATCTAAGTGTGTGTA CHI=IAIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIICIFIH AS:C:166 At the position of your snp of interest, rs1872067 at 163076840, these Neandertal outputs match what you observed in the browser: G. I hope this is helpful. Please contact the mail list ([email protected]) again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group On 8/10/11 11:34 AM, Claudia Moreau wrote: > Hi, > > > > I would like to know why a Neanderthal position in the UCSC browser can be > different than in the BAM sequence in the tables section of UCSC. I attached > what I had in the browser. My concern is about position 163076840 on chr4 > (rs1872067). > > > > Here is the sequence that I obtained for human: > > > >> hg18_snp130_rs1872067 range=chr4:163076830-163076850 5'pad=10 3'pad=10 > strand=+ repeatMasking=none > > AATGAAAGTT C TTTTGCATAT > > > > > > Here is the sequence that I obtained for Neanderthal Vi33.26 which seem to > be the only one with a sequence for this position: > > > >> hg18_bamSLVi33dot26_C_M_SOLEXA-GA02_JK_PE51_SL29_SL30_SL31_rep:3:87:1372:18 > 37 range=chr4:163076828-163076901 5'pad=10 3'pad=10 strand=+ > repeatMasking=none > GCAATGAAAGTT C TTTTGCATATATCTACACATATACATAATTTACATAATCTAAGTGTGTGTATGTATGTGTA > > > > > > Here is the sequence that I obtained for Neanderthal ctg which is the same > as Vi33.26: > > > >> hg18_bamAll_all-hg18_11118948 range=chr4:163076828-163076901 5'pad=10 > 3'pad=10 strand=+ repeatMasking=none > GCAATGAAAGTT C TTTTGCATATATCTACACATATACATAATTTACATAATCTAAGTGTGTGTATGTATGTGTA > > Thanks a lot, > > > > > Claudia Moreau > > Assistante de recherche, laboratoire de génétique des populations > > Hôpital Ste-Justine > > 3175 Chemin de la Côte-Ste-Catherine, pavillon Charles-Bruneau B-477 > > Montréal H3T 1C5 > > tel: 514-345-4931 ext 2974 > > FAX: 514-345-4731 > > > > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
