Table 4 Prior and post-filtering transcriptome summary statistics for potato cultivar-specific coding sequences generated by TransRate.
From: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato
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% |
