Table 4. Processing SNP markers for QTL analysis.
| S. no. | SNP calling | MPs | ||
|---|---|---|---|---|
| HAN × WTR-1 | CH448 × WTR-1 | Z413 × WTR-1 | ||
| 1 | Raw SNPs | 10,432 | 14,117 | 7,865 |
| 2 | Quality base filtering at LMD50 | 4,666 | 5,957 | 3,147 |
| 3 | Removed heterozygous alleles in both parents | 345 | 483 | 454 |
| 4 | Removed mono-morphic alleles in both parents | 35 | 1,852 | 83 |
| 5 | SNP markers for QTL analysis | 4,286 | 3,622 | 2,610 |
| 6 | Exclusion of redundant markers | 1,504 | 1,617 | 1,249 |
| 7 | Number of markers used for linkage map construction | 2,782 | 2,005 | 1,361 |
| 8 | Removed markers with χ2 >6.0 of segregation distortion | 1,608 | 895 | 527 |
| 9 | Number of SNP markers used for ICIM-ADD | 1,174 | 1,110 | 834 |