Table 3 Transcriptome quality control by RNA-seq reads remapping.
From: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato
Mapping statistics/genotype | Désirée’ | PW363’ | Rywal’ |
|---|---|---|---|
Number of input reads | 177,149,132 | 52,171,015 | 342,767,035 |
Average input read length | 178 | 179 | 199 |
UNIQUE READS: | |||
Uniquely mapped reads number | 64,507,790 | 18,416,487 | 206,003,021 |
Uniquely mapped reads# % | 36% | 35% | 60% |
Average mapped length | 175 | 176 | 196 |
Number of splices*: Total | 496,170 | 267,268 | 1,700,235 |
Number of splices*: Annotated (sjdb) | 0 | 0 | 0 |
Number of splices*: GT/AG | 258,208 | 105,551 | 1,162,885 |
Number of splices*: GC/AG | 10,749 | 5,693 | 79,495 |
Number of splices*: AT/AC | 1,486 | 2,192 | 1,840 |
Number of splices*: Non-canonical | 225,727 | 153,832 | 456,015 |
Mismatch rate per base % | 0.50% | 0.53% | 0.59% |
Deletion rate per base | 0.03% | 0.03% | 0.03% |
Deletion average length | 2.72 | 2.53 | 3.02 |
Insertion rate per base | 0.02% | 0.02% | 0.03% |
Insertion average length | 1.93 | 1.86 | 1.91 |
MULTI-MAPPING READS: | |||
Number of reads mapped to multiple loci | 98,694,222 | 29,366,122 | 108,669,657 |
% of reads mapped to multiple loci# | 56% | 56% | 32% |
Number of reads mapped to too many loci | 4,652,918 | 1,555,704 | 1,541,238 |
% of reads mapped to too many loci | 2.63% | 2.98% | 0.45% |
UNMAPPED READS: | |||
% of reads unmapped: too many mismatches | 0% | 0% | 0% |
% of reads unmapped: too short | 5.25% | 5.43% | 7.75% |
% of reads unmapped: other | 0% | 0% | 0% |
CHIMERIC READS: | |||
Number of chimeric reads | 0 | 0 | 0 |
% of chimeric reads | 0% | 0% | 0% |
