Table 3 Statistics on SNPs/InDels identified between the samples and the reference.
Genotype | Total SNPs identified | Transition | Transversions | Triallelic SNPs | Number of SNPs after filtration | Genic SNPs |
|---|---|---|---|---|---|---|
JI220 | 294,956 | 167,623 | 78,092 | 51 | 55,587 | 29,439 |
JC12 | 929,114 | 577,558 | 245,896 | 24 | 63,221 | 84,792 |
TMV5 | 713,512 | 453,056 | 192,247 | 9 | 74,178 | 73,923 |
RG72 | 644,037 | 406,047 | 172,030 | 5 | 82,802 | 62,838 |
RG3309 | 852,482 | 225,033 | 538,652 | 6 | 105,300 | 80,195 |
DPC9 | 604,063 | 380,789 | 161,192 | 6 | 78,457 | 56,241 |
RG43 | 387,296 | 235,152 | 100,703 | 27 | 62,842 | 32,010 |
48-1 | 592,812 | 373,094 | 160,160 | 4 | 78,747 | 61,035 |
RG1139 | 490,382 | 295,749 | 129,786 | 2 | 74,252 | 63,802 |
RG2787 | 670,889 | 423,464 | 176,940 | 11 | 88,115 | 60,934 |
RG2819 | 672,843 | 425,258 | 178,583 | 10 | 88,806 | 61,609 |
VP1 | 440,832 | 266,069 | 118,137 | 2 | 73,224 | 53,660 |
DCS9 | 305,433 | 187,765 | 90,138 | 0 | 111,179 | 39,500 |
RG3216 | 415,777 | 117,476 | 56,680 | 0 | 74,089 | 63,916 |
