Table 4 Detailed interpretations for high False Discovery Rate and False Negative rate
False Discovery Rate (FDR) class | Â | Â |
|---|---|---|
Intersection of the reasons | Number of loci (percentage) | In dbSNP v129 |
Reasonable interpretations for SNPs filtered out in YH WGS results | 29,687(83.38%) | 23,348(78.65%) |
   1. Low depth (<2) | 394(1.11%) | --- |
   2. Low quality (< 20) | 10,920(30.67%) | --- |
   3. High copy number (> 2) | 25,036(70.32%) | --- |
   4. High depth (> 200) | 538(1.51%) | --- |
Overcalled for unknown reasons in RRL sequencing | 5,916(16.61%) | 615(10.40%) |
False Negative rate (FNR) class | Â | Â |
Intersection of the reasons | Number of loci (percentage) | In dbSNP v129 |
Reasonable interpretations for SNPs filtered out in RRL sequencing results | 57,169(74.11%) | 45,216(79.09%) |
   1. Low depth (<2) | 29,478(38.22%) | --- |
   2. Low quality (< 20) | 53,830(69.79%) | --- |
   3. High copy number (> 2) | 25,587(33.17%) | --- |
   4. High depth (> 200) | 43(0.06%) | --- |
Allele dropout in RRL sequencing | 19,967(25.89%) | 10,724(53.71%) |