SNP comparisons

SNP comparisons

• Using positions only

• Comparing Watson, Venter, dbSNP– Watson more conservative in calls– I used Venter method 1 calls (placed unambiguously)

• Venter Indels• Ensembl made their own SNP calls for Watson and

Venter

SNPsdbSNP 12,350,000Venter 3,325,000Watson 2,060,000

1,817,000

10, 000

210,000476,000

Venter and Watson each have 3 variants that are in LSDBs.

233,000

1,032,000

SNP density (SNPs/kb)

ORegAnno (regions from 1 bp to over 5000 bps)

– 5,391 (Venter 7,253) SNPs that overlap ORegAnno– 3,519 (3,956) ORegAnno regions overlap the SNPs

• 2,571 ORegAnno regions are the same

– 27 (36) are in 1 bp regions• All are also in dbSNP• 11 are same

Venter’s Indels• 486,598 non-dbSNP variants– 280,722 SNPs– 205,875 indels

• Only 94 of these are in coding exons– 65 are frame shifts

» Found GO terms for 41 entries.» 37 cellular» 33 function» 34 process» GO:0005515 {14} protein binding (Molecular function)» GO:0016020 {13} membrane (Cellular component)» GO:0005634 {13} nucleus (Cellular component)» GO:0016021 {9} integral to membrane (Cellular

component)» GO:0005622 {7} intracellular (Cellular component)» GO:0004872 {7} receptor activity (Molecular function)» GO:0005509 {6} calcium ion binding (Molecular function)

Ensembl

• Ensembl made their own calls on the SNPs from Venter and Watson’s sequences– Need Ensembl 49 for accurate Venter SNPs

Ensembl Venter and Venter method1

2,602,17895% in dbSNP

723,35256% in dbSNP766,195

64% in dbSNP

dbSNP 128 chromosome reports

Ensembl Watson and Watson

1,602,563100% in dbSNP

457,98153% in dbSNP

798,567100% in dbSNP

dbSNP 128 chromosome reports

SNP density with Ensembl calls

Percent of SNPs by location

SNPs in Ultra Conserved Regions• dbSNP 128 has 168 • Watson and Venter have 25– 16 of which are in dbSNP– 9 new (none from Ensembl)

• chr1 115081716 W• chr1 115081717 W• chr1 50872068 W• chr3 153647146 W• chr6 163911701 V• chr9 139162434 W• chr11 8274734 W• chr15 65665291 V• chr18 21119518 W

SNPs in Ultra conserved regions

• 3 % of Ultra conserved regions have either Watson or Venter SNPs

• 25 % of Ultra conserved regions have SNPs from dbSNP 128 (168 SNPs), most have 1 or 2– With a maximum of 12 SNPs in one region– A runner up of 5 SNPs in one region

UC with 12 SNPs

What’s in Ultra Conserved regions?

• Total 481 region– 480 have conserved TFBS– 168 have Vista Enhancers from LBNL– 72 have coding exons (only 19 with SNPs)– 124 have SNPs (dbSNP 128)

• 2 more interesting UCs– UC without a conserved TFBS– UC with TFBS, SNP, Coding, and Repeat masker

UC without conserved TFBS

UC with TFBS, SNP, RM, Coding

SNPs in Conserved TFBS

• About 3% of the 3.8 million binding sites have SNPs in dbSNP 128

• About 3% of the .8 million binding sites with a z score >= 2.33 have SNPs in dbSNP 128

SNP density

This is computed on a 10kb window. The weighted average is computed for each window.

SNP density with Ensembl

SNPs in ORegAnno regions

SNPs in ORegAnno regions

SNPs in ORegAnno regions

Of the 9,427 ORegAnno regions (excluding TFBS), 1,603 of them have no SNPs from dbSNP 126 (from UCSC).

SNPs in ORegAnno regions

SNPs per exonVenter SNPsPercentages close in both Venter’s set and Ensembl’s.93 % none5% 1 SNP2% >1 SNP

The End

SNP locations nt counts• Watson 2,060,544 • Venter method 1

3,325,530

SNP density Min and Max from last slide, plus dbSNP 126

Percent of SNPs by location

SNP coverageThis is computed on 10kb non-overlapping windows. If there is 1 SNP in the window it gets a 1 otherwise a zero. The darker areas indicate sections where it jumps between 0 and 1 more often. A white area with a blue line at the top has at least 1 SNP per 10kb consistently.

UCSC Genome Browser