I can't find this ...
in those typical hapmap files from
ftp://ftp.ncbi.nlm.nih.gov/hapmap/ge...I+III/forward/
like:
(blanks replaced with comma)
what do the double-letter entries mean ?
that sample (=person) has one of the 2 letters at that position in that chromosome ? which of the two ?
ACGT
(N=not available)
more keywords for google:
98,185,150,120,112,127,121,97,195,113,220 total=1417
of such entries in the 11 populations
asw,ceu,chb,chd,gih,jpt,lwk,mex,mkk,tsi,yri
found this comparison, Mar,2012, 1000 genomes vs. hapmap
found another thread that counts ~15M SNPs via hapmap
but I get in that directory ~4.3M SNP-positions only
so far I have SNP-positions:
20:124241
01:326089
02:337596
21:54065
22:59327
10:218893
_x:126192
_y:1032
_m:214
no google-hits with these numbers
do I really need all chromosomes
in those typical hapmap files from
ftp://ftp.ncbi.nlm.nih.gov/hapmap/ge...I+III/forward/
like:
(blanks replaced with comma)
Code:
rs#,alleles,chrom,pos,strand,assembly#,center,protLSID,assayLSID,panelLSID,QCcode,NA06984,...,NA12892 rs28412942,A/T,chrM,410,+,ncbi_B36,affymetrix,urn:LSID:affymetrix.hapmap.org:Protocol:GenomeWideSNP_6.0:2,urn:LSID:affymetrix.hapmap.org:Assay:SNP_A-8575126:2,urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1,QC+,NN,TT,NN,NN,TT,TT,TT,NN,NN,TT,NN,TT,TT,TT,NN,TT,NN,NN,TT,NN,TT,TT,TT,NN,NN,TT,NN,TT,NN,NN,TT,TT,NN,NN,TT,TT,NN,NN,NN,TT,AA,NN,TT,NN,NN,TT,TT,TT,TT,TT,TT,TT,TT,NN,NN,TT,TT,TT,TT,TT,TT,NN,TT,TT,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,TT,TT,TT,TT,TT,TT,TT,TT,TT,TT,NN,TT,TT,TT,TT,TT,TT,TT,TT,TT,NN,AA,TT,TT,TT,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,TT,NN,TT,TT,NN,NN,TT,NN,NN,TT,TT,TT,TT,TT,TT,TT,TT,NN,NN,NN,NN,NN,NN,TT,TT,TT,TT,TT,TT,NN,NN,NN,NN,NN,NN,NN,NN,NN,TT,TT,TT,TT,TT,TT,NN,TT,NN,NN,TT,TT rs3937039,A/G,chrM,665,+,ncbi_b36,broad,urn:lsid:wicgr.hapmap.org:Protocol:genotype_protocol_1:1,urn:lsid:wicgr.hapmap.org:Assay:MITOCHONDRIA-mt663:1,urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1,QC+,NN,AA,NN,NN,AA,AA,AA,NN,NN,AA,NN,AA,AA,AA,NN,AA,NN,NN,AA,NN,AA,AA,AA,NN,NN,AA,NN,AA,NN,AA,AA,AA,NN,NN,AA,AA,NN,NN,NN,AA,AA,NN,AA,NN,NN,AA,AA,AA,AA,AA,AA,AA,AA,NN,NN,AA,AA,AA,AA,AA,AA,NN,AA,AA,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,AA,AA,AA,AA,AA,AA,AA,AA,AA,AA,NN,AA,AA,AA,AA,AA,AA,AA,AA,AA,AA,AA,AA,AA,AA,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,AA,NN,AA,AA,NN,NN,AA,NN,NN,AA,AA,NN,AA,AA,AA,AA,AA,NN,NN,NN,NN,NN,NN,AA,AA,AA,AA,AA,AA,NN,NN,NN,NN,NN,NN,NN,NN,NN,AA,AA,AA,AA,AA,AA,NN,AA,NN,NN,AA,AA rs2853517,A/G,chrM,711,+,ncbi_b36,broad,urn:lsid:wicgr.hapmap.org:Protocol:genotype_protocol_1:1,urn:lsid:wicgr.hapmap.org:Assay:MITOCHONDRIA-mt709:1,urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1,QC+,NN,GG,NN,NN,GG,GG,GG,NN,NN,AA,NN,AA,GG,AA,NN,GG,NN,NN,NN,NN,GG,AA,GG,NN,NN,GG,NN,GG,NN,GG,GG,GG,NN,NN,GG,GG,NN,NN,NN,GG,GG,NN,GG,NN,NN,GG,GG,GG,GG,GG,GG,GG,GG,NN,NN,NN,GG,GG,GG,GG,GG,NN,GG,GG,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,GG,GG,AA,GG,AA,GG,AA,GG,AA,GG,NN,GG,GG,GG,GG,GG,GG,AA,GG,GG,GG,GG,NN,GG,GG,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,GG,NN,GG,GG,NN,NN,GG,NN,NN,AA,GG,GG,AA,GG,GG,AA,AA,NN,NN,NN,NN,NN,NN,GG,GG,GG,GG,GG,GG,NN,NN,NN,NN,NN,NN,NN,NN,NN,GG,GG,GG,GG,GG,GG,NN,GG,NN,NN,GG,GG rs28358568,C/T,chrM,712,+,ncbi_b36,broad,urn:lsid:wicgr.hapmap.org:Protocol:genotype_protocol_1:1,urn:lsid:wicgr.hapmap.org:Assay:MITOCHONDRIA-mt710:1,urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1,QC+,NN,TT,NN,NN,TT,TT,TT,NN,NN,TT,NN,TT,TT,TT,NN,TT,NN,NN,NN,NN,TT,TT,TT,NN,NN,TT,NN,TT,NN,TT,TT,TT,NN,NN,TT,TT,NN,NN,NN,TT,TT,NN,TT,NN,NN,TT,TT,TT,TT,TT,TT,TT,TT,NN,NN,TT,TT,TT,TT,TT,TT,NN,TT,TT,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,TT,TT,TT,TT,TT,TT,TT,TT,TT,TT,NN,TT,TT,TT,TT,TT,TT,TT,TT,TT,NN,TT,TT,TT,TT,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,TT,NN,TT,TT,NN,NN,TT,NN,NN,TT,TT,TT,TT,TT,TT,TT,TT,NN,NN,NN,NN,NN,NN,TT,TT,TT,TT,TT,TT,NN,NN,NN,NN,NN,NN,NN,NN,NN,TT,TT,TT,TT,TT,TT,NN,TT,NN,NN,TT,TT rs2853519,A/G,chrM,771,+,ncbi_B36,affymetrix,urn:LSID:affymetrix.hapmap.org:Protocol:GenomeWideSNP_6.0:2,urn:LSID:affymetrix.hapmap.org:Assay:SNP_A-8574695:2,urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1,QC+,NN,GG,NN,NN,GG,GG,GG,NN,NN,GG,NN,GG,GG,GG,NN,GG,NN,NN,GG,NN,GG,GG,GG,NN,NN,GG,NN,GG,NN,GG,GG,GG,NN,NN,GG,GG,NN,NN,NN,GG,GG,NN,GG,NN,NN,GG,GG,GG,GG,GG,GG,GG,GG,NN,NN,GG,GG,GG,GG,GG,GG,NN,GG,GG,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,GG,GG,GG,GG,GG,GG,GG,GG,GG,GG,NN,GG,GG,GG,GG,GG,GG,GG,GG,GG,GG,GG,GG,GG,GG,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,GG,NN,GG,GG,NN,NN,GG,NN,NN,GG,GG,GG,GG,GG,GG,GG,GG,NN,NN,NN,NN,NN,NN,GG,GG,GG,GG,GG,GG,NN,NN,NN,NN,NN,NN,NN,NN,NN,GG,GG,GG,GG,GG,GG,NN,GG,NN,NN,GG,GG rs2853520,A/T,chrM,827,+,ncbi_b36,broad,urn:lsid:wicgr.hapmap.org:Protocol:genotype_protocol_1:1,urn:lsid:wicgr.hapmap.org:Assay:MITOCHONDRIA-mt825:1,urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1,QC+,NN,TT,NN,NN,TT,TT,TT,NN,NN,TT,NN,TT,TT,TT,NN,TT,NN,NN,TT,NN,TT,TT,TT,NN,NN,TT,NN,TT,NN,TT,TT,TT,NN,NN,TT,TT,NN,NN,NN,TT,TT,NN,TT,NN,NN,TT,TT,TT,TT,TT,TT,TT,TT,NN,NN,TT,TT,TT,TT,TT,TT,NN,TT,TT,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,TT,TT,TT,TT,TT,TT,TT,TT,TT,TT,NN,TT,TT,TT,TT,TT,TT,TT,TT,TT,TT,TT,TT,TT,TT,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,TT,NN,TT,TT,NN,NN,TT,NN,NN,TT,TT,TT,TT,TT,TT,TT,TT,NN,NN,NN,NN,NN,NN,TT,TT,TT,TT,TT,TT,NN,NN,NN,NN,NN,NN,NN,NN,NN,TT,TT,TT,TT,TT,TT,NN,TT,NN,NN,TT,TT rs28358570,C/T,chrM,923,+,ncbi_B36,affymetrix,urn:LSID:affymetrix.hapmap.org:Protocol:GenomeWideSNP_6.0:2,urn:LSID:affymetrix.hapmap.org:Assay:SNP_A-8574945:2,urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1,QC+,NN,TT,NN,NN,TT,TT,TT,NN,NN,TT,NN,TT,TT,TT,NN,TT,NN,NN,TT,NN,TT,TT,TT,NN,NN,TT,NN,TT,NN,TT,TT,TT,NN,NN,TT,TT,NN,NN,NN,TT,TT,NN,TT,NN,NN,TT,TT,TT,TT,TT,TT,TT,TT,NN,NN,TT,TT,TT,TT,TT,TT,NN,TT,TT,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,TT,TT,TT,TT,TT,TT,TT,TT,TT,TT,NN,TT,TT,TT,TT,TT,TT,TT,TT,TT,TT,TT,TT,TT,TT,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,TT,NN,TT,TT,NN,NN,TT,NN,NN,TT,TT,TT,TT,TT,TT,TT,TT,NN,NN,NN,NN,NN,NN,TT,TT,TT,TT,TT,TT,NN,NN,NN,NN,NN,NN,NN,NN,NN,TT,TT,TT,TT,TT,TT,NN,TT,NN,NN,TT,TT rs2856982,A/G,chrM,1020,+,ncbi_B36,affymetrix,urn:LSID:affymetrix.hapmap.org:Protocol:GenomeWideSNP_6.0:2,urn:LSID:affymetrix.hapmap.org:Assay:SNP_A-8574722:2,urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1,QC+,NN,GG,NN,NN,GG,GG,GG,NN,NN,GG,NN,GG,GG,GG,NN,GG,NN,NN,GG,NN,GG,GG,GG,NN,NN,GG,NN,GG,NN,GG,GG,GG,NN,NN,GG,GG,NN,NN,NN,GG,GG,NN,GG,NN,NN,GG,GG,GG,GG,GG,GG,GG,GG,NN,NN,GG,GG,GG,GG,GG,GG,NN,GG,GG,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,GG,GG,GG,GG,GG,GG,GG,GG,GG,GG,NN,GG,GG,GG,GG,GG,GG,GG,GG,GG,GG,GG,GG,GG,GG,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,GG,NN,GG,GG,NN,NN,GG,NN,NN,GG,GG,GG,GG,GG,GG,GG,GG,NN,NN,NN,NN,NN,NN,GG,GG,GG,GG,GG,GG,NN,NN,NN,NN,NN,NN,NN,NN,NN,GG,GG,GG,GG,GG,GG,NN,GG,NN,NN,GG,GG rs2000974,C/T,chrM,1050,+,ncbi_B36,affymetrix,urn:LSID:affymetrix.hapmap.org:Protocol:GenomeWideSNP_6.0:2,urn:LSID:affymetrix.hapmap.org:Assay:SNP_A-8574535:2,urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1,QC+,NN,CC,NN,NN,CC,CC,CC,NN,NN,CC,NN,CC,CC,CC,NN,CC,NN,NN,CC,NN,CC,CC,CC,NN,NN,CC,NN,CC,NN,CC,CC,CC,NN,NN,CC,CC,NN,NN,NN,CC,CC,NN,CC,NN,NN,CC,CC,CC,CC,CC,CC,CC,CC,NN,NN,CC,CC,CC,CC,CC,CC,NN,CC,CC,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,CC,CC,CC,CC,CC,CC,CC,CC,CC,CC,NN,CC,CC,CC,CC,CC,CC,CC,CC,CC,CC,CC,CC,CC,CC,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,CC,NN,CC,CC,NN,NN,CC,NN,NN,CC,CC,CC,CC,CC,CC,CC,CC,NN,NN,NN,NN,NN,NN,CC,CC,CC,CC,CC,CC,NN,NN,NN,NN,NN,NN,NN,NN,NN,CC,CC,CC,CC,CC,CC,NN,CC,NN,NN,CC,CC rs28358571,C/T,chrM,1191,+,ncbi_b36,broad,urn:lsid:wicgr.hapmap.org:Protocol:genotype_protocol_1:1,urn:lsid:wicgr.hapmap.org:Assay:MITOCHONDRIA-mt1189:1,urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1,QC+,NN,TT,NN,NN,TT,TT,TT,NN,NN,TT,NN,TT,TT,TT,NN,TT,NN,NN,TT,NN,TT,TT,TT,NN,NN,TT,NN,TT,NN,TT,TT,TT,NN,NN,TT,TT,NN,NN,NN,CC,TT,NN,TT,NN,NN,TT,TT,TT,TT,TT,TT,TT,TT,NN,NN,TT,TT,TT,TT,TT,TT,NN,TT,TT,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,TT,TT,TT,TT,TT,TT,TT,TT,TT,TT,NN,TT,TT,TT,CC,TT,TT,TT,TT,TT,TT,TT,TT,TT,TT,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,TT,NN,TT,TT,NN,NN,TT,NN,NN,TT,TT,TT,TT,TT,TT,TT,TT,NN,NN,NN,NN,NN,NN,TT,TT,TT,TT,TT,TT,NN,NN,NN,NN,NN,NN,NN,NN,NN,TT,TT,TT,TT,TT,TT,NN,TT,NN,NN,TT,TT rs28358572,C/T,chrM,1245,+,ncbi_b36,broad,urn:lsid:wicgr.hapmap.org:Protocol:genotype_protocol_1:1,urn:lsid:wicgr.hapmap.org:Assay:MITOCHONDRIA-mt1243:1,urn:lsid:dcc.hapmap.org:Panel:CEPH-30-trios:1,QC+,NN,TT,NN,NN,TT,TT,TT,NN,NN,TT,NN,CC,TT,TT,NN,TT,NN,NN,NN,NN,TT,CC,TT,NN,NN,TT,NN,TT,NN,TT,TT,TT,NN,NN,TT,TT,NN,NN,NN,TT,TT,NN,TT,NN,NN,TT,TT,TT,TT,TT,TT,TT,TT,NN,NN,NN,TT,TT,TT,TT,TT,NN,TT,TT,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,TT,TT,TT,TT,TT,TT,TT,TT,TT,TT,NN,TT,TT,TT,TT,TT,TT,TT,TT,TT,TT,TT,TT,TT,TT,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,NN,TT,NN,TT,TT,NN,NN,TT,NN,NN,TT,TT,TT,TT,TT,TT,TT,TT,NN,NN,NN,NN,NN,NN,TT,TT,TT,TT,TT,TT,NN,NN,NN,NN,NN,NN,NN,NN,NN,TT,TT,TT,TT,TT,TT,NN,TT,NN,NN,TT,TT ...
what do the double-letter entries mean ?
that sample (=person) has one of the 2 letters at that position in that chromosome ? which of the two ?
ACGT
(N=not available)
more keywords for google:
98,185,150,120,112,127,121,97,195,113,220 total=1417
of such entries in the 11 populations
asw,ceu,chb,chd,gih,jpt,lwk,mex,mkk,tsi,yri
found this comparison, Mar,2012, 1000 genomes vs. hapmap
found another thread that counts ~15M SNPs via hapmap
but I get in that directory ~4.3M SNP-positions only
so far I have SNP-positions:
20:124241
01:326089
02:337596
21:54065
22:59327
10:218893
_x:126192
_y:1032
_m:214
no google-hits with these numbers
do I really need all chromosomes
Comment