A bioinformatics approach to distinguish plant parasite and host transcriptomes in interface tissue by classifying RNA-Seq reads

Table 5 Assessment for the rate of misclassification of reads by mapping Cj_nc_reads and Gm_nc_reads onto two contig sets

A.	Contig set	Merged set of Cj_contigs_cg1 and Gmax_275_Wm82.a2.v1.transcript
	Classification	Reads mapped onto C. japonica (%)^a	Reads mapped onto G.max (%)^a	AUC^b
	Mapped reads (number)	Number of reads (%))
	Cj_nc_reads	54,936,999	187	0.999
	(114,056,994)	(48.2)	(0.00016)
	Gm_nc_reads	1,791	25,880,696
	(28,728,782)	(0.0062)	(80.9)
B.	Contig set	Merged set of Cj_contigs_cg2 and Gmax_275_Wm82.a2.v1.transcript
	Classification	Reads mapped onto C. japonica (%)^a	Reads mapped onto G.max (%)^a	AUC^b
	Mapped reads (number)	Number of reads (%)
	Cj_nc_reads	52,486,992	191	0.955
	(114,056,994)	(46.0)	(0.00017)
	Gm_nc_reads	2,377,249	24,253,863
	(28,728,782)	(8.27)	(84.4)

^aNumbers indicate percentage of mapped reads to the total number of resds. ^bAUC; area under receiver operating characteristic (ROC) curve.
Mapping parameter was as follows; In Panel A and Panel B, match length ≥90 bp and at most 1 mismatch and 1 gap allowed.

ISSN: 1746-4811