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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

From: Searching for SNPs with cloud computing

       (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%
  1. '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.