Table 4.
Prior and post-filtering transcriptome summary statistics for potato cultivar-specific coding sequences generated by TransRate.
| TransRate metrics | Désirée | PW363 | Rywal | |||
|---|---|---|---|---|---|---|
| Pre-filter (initial) | Post-filter | Pre-filter (initial) | Post-filter | Pre-filter (initial) | Post-filter | |
| CONTIG METRICS | ||||||
| No. sequences | 350,271 | 197,839 | 273,216 | 159,278 | 134,755 | 79,095 |
| Sequence mean length | 504 | 792 | 516 | 775 | 459 | 707 |
| No. sequences under 200 nt | 125,465 | 25,330 | 88,230 | 17,370 | 52,653 | 13,198 |
| No. sequences over 1000 nt | 57,679 | 55,837 | 44,508 | 42,571 | 19,175 | 18,748 |
| No. sequences over 10000 nt | 23 | 23 | 3 | 3 | 1 | 1 |
| ’n90 | 369 | 444 | 366 | 429 | 351 | 390 |
| ’n50 | 1,194 | 1,209 | 1,110 | 1,131 | 1,227 | 1,218 |
| GC % | 41% | 42% | 42% | 42% | 42% | 42% |
| Ambiguous nucleotide (N) % | 0% | 0% | 0% | 0% | 0% | 0% |
| COMPARATIVE METRICS | ||||||
| No. seq. with CRBB hits* | 160,295 | 138,131 | 138,443 | 116,834 | 66,258 | 55,239 |
| No. reference seq. with CRBB hits* | 29,858 | 27,642 | 25,739 | 23,839 | 23,549 | 22,163 |
| coverage50#* | 25,991 | 24,586 | 21,875 | 20,620 | 20,258 | 19,538 |
| coverage95#* | 19,329 | 18,246 | 15,664 | 14,727 | 14,967 | 14,470 |
| Reference coverage* | 65% | 63% | 56% | 54% | 53% | 52% |
’The largest contig size at which at least 90% or 50% of bases are contained in contigs at least this length.
*Reference-based summary statistics (merged Phureja DM coding sequences were used as reference).
#Proportion of reference proteins with at least N% of their bases covered by a Conditional Reciprocal Best Blast (CRBB) hit.