Table 6. Alignments of RNA-seq reads to the CS reference genome and SNP calling.
| Line | Short reads | Number of filtered short reads | Alignment reads (%) | SNPs |
|---|---|---|---|---|
| PI476874 | 669383 | 348976 | 179414 (51.41%) | 143 |
| AT47 | 4972932 | 3076553 | 2763303 (89.81%) | 58276 |
| Ldn | 6316174 | 4365490 | 3961770 (90.75%) | 40864 |
| Yukichikara | 5704291 | 3235890 | 3006678 (92.92%) | 14984 |
| SB3#3 | 6770706 | 3820073 | 3529836 (92.40%) | 20831 |
| SB11-1#3 | 5968875 | 3498880 | 3240623 (92.62%) | 16888 |
| SB11-2#3 | 5403372 | 3106937 | 2859040 (92.03%) | 17284 |
| Kitanokaori | 5648886 | 3169954 | 2903478 (91.60%) | 15900 |
| SB9#2 | 5387783 | 3340342 | 3081828 (92.26%) | 21751 |
| SB16-1#1 | 6240674 | 3865559 | 3555322 (91.98%) | 20924 |
| SB16-1#2 | 5446262 | 3405431 | 3144968 (92.35%) | 20183 |
| Haruyokoi | 6343349 | 3602895 | 3360936 (93.29%) | 17818 |
| SB12#1 | 6315944 | 3635296 | 3371723 (92.75%) | 19418 |
| SB13-2#1 | 5381735 | 3201166 | 2942918 (91.94%) | 19974 |
| Haruhinode | 5998712 | 3522788 | 3267708 (92.76%) | 15775 |
| SB14#3 | 5123579 | 2921022 | 2709816 (92.77%) | 13753 |