Table 2 |
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|
SNP calling measurements for Crossbow experiments using simulated reads from human chromosomes 22 and X |
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|
Chromosome 22 |
Chromosome X |
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|
|
|
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|
True number of sites |
Crossbow sensitivity |
Crossbow precision |
True number of sites |
Crossbow sensitivity |
Crossbow precision |
|
|
|
||||||
|
All SNP sites |
46,586 |
99.0% |
99.1% |
102,219 |
99.0% |
99.6% |
|
Only HapMap SNP sites |
36,096 |
99.8% |
99.9% |
71,976 |
99.9% |
99.9% |
|
Only novel SNP sites |
10,490 |
96.3% |
96.3% |
30,243 |
96.8% |
98.8% |
|
Only homozygous |
14,858 |
98.7% |
99.9% |
NA |
NA |
NA |
|
Only heterozygous |
31,728 |
99.2% |
98.8% |
NA |
NA |
NA |
|
Only novel het |
6,967 |
96.6% |
94.6% |
NA |
NA |
NA |
|
All other |
39,619 |
99.4% |
99.9% |
NA |
NA |
NA |
|
|
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|
Sensitivity is the proportion of true SNPs that were correctly identified. Precision is the proportion of called SNPs that were genuine. NA denotes "not applicable" because of the ploidy of the chromosome. |
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|
Langmead et al. Genome Biology 2009 10:R134 doi:10.1186/gb-2009-10-11-r134 |
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