Table 3.

Transcriptome quality control by RNA-seq reads remapping.

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%

Illumina paired-end reads used for generating assemblies were mapped back to the corresponding cultivar specific transcriptomes using STAR.

*Number of reads crossing supposed splice sites.

‘Initially constructed transcriptomes (prior to filtering steps).

^#Relevant % of mapped reads: % of uniquely mapped reads + % of reads mapped to multiple loci.