Table 5 Summary statistics for potato cultivar-specific representative transcript sequences generated by TransRate.

From: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato

TransRate metrics

Désirée

PW363

Rywal

PGSC+

CONTIG METRICS

No. sequences

57,943

43,883

36,336

39,031

Sequence mean length

922

926

1,028

1,283

No. sequences under 200 nt

875

1,377

1,310

87

No. sequences over 1000 nt

18,500

14,545

14,307

20,226

No. sequences over 10000 nt

13

6

2

0

’n90

369

387

440

645

’n50

1,566

1,535

1,673

1,726

GC %

40%

41%

41%

40%

Ambiguous nucleotide (N) %

0%

0%

0%

0%

COMPARATIVE METRICS

No. seq. with CRBB hits*

38,034

30,826

28,389

38,600

No. reference seq. with CRBB hits*

25,094

21,751

21,299

37,534

coverage50#*

12,799

10,693

7,909

36,379

coverage95#*

8,053

6,430

5,053

30,187

Reference coverage*

33%

28%

20%

75%

  1. ’The largest contig size at which at least 90% or 50% of bases are contained in contigs at least this length.
  2. *Reference-based summary statistics (merged Phureja DM coding sequences were used as reference).
  3. #Proportion of reference proteins with at least N% of their bases covered by a Conditional Reciprocal Best Blast (CRBB) hit.
  4. +PGSC_DM_v3.4_transcript-update_representative.fasta.zip file from Spud DB was used for Phureja-specific representative transcript sequences (PGSC).
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