Table 3

Coverage and agreement measurements comparing Crossbow (CB) and SOAP/SOAPsnp (SS) to the genotyping results obtained by an Illumina 1 M genotyping assay in the SOAPsnp study

(SS)

(CB)



Illumina 1 M genotype

Sites

Sites covered (SS)

Sites covered (CB)

Agreed (SS)

Agreed (CB)

Missed allele

Other disagreement

Missed allele

Other disagreement


Chromosome X

HOM reference

27,196

98.65%

99.83%

99.99%

99.99%

NA

0.004%

NA

0.011%

HOM mutant

10,737

98.49%

99.19%

99.89%

99.85%

NA

0.113%

NA

0.150%

Total

37,933

98.61%

99.65%

99.97%

99.95%

NA

0.035%

NA

0.050%

Autosomal

HOM reference

540,878

99.11%

99.88%

99.96%

99.92%

NA

0.044%

NA

0.078%

HOM mutant

208,436

98.79%

99.28%

99.81%

99.70%

NA

0.194%

NA

0.296%

HET

250,667

94.81%

99.64%

99.61%

99.75%

0.374%

0.017%

0.236%

0.014%

Total

999,981

97.97%

99.70%

99.84%

99.83%

0.091%

0.069%

0.059%

0.108%


'Sites covered' is the proportion of BeadChip sites covered by a sufficient number of sequencing reads (roughly four reads for diploid and two reads for haploid chromosomes). 'Agreed' is the proportion of covered BeadChip sites where the BeadChip call equaled the SOAPsnp/Crossbow call. 'Missed allele' is the proportion of covered sites where SOAPsnp/Crossbow called a position as homozygous for one of two heterozygous alleles called by BeadChip. 'Other disagreement' is the proportion of covered sites where the BeadChip call differed from the SOAPsnp/Crossbow in any other way. NA denotes "not applicable" due to ploidy.

Langmead et al. Genome Biology 2009 10:R134   doi:10.1186/gb-2009-10-11-r134

Open Data