Table 3 |
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|
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. |
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|
Langmead et al. Genome Biology 2009 10:R134 doi:10.1186/gb-2009-10-11-r134 |
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