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Table 2 Assessment for the rate of misclassification of reads by mapping Cj_nc_reads and Ib_nc_reads onto two transcript sets

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

A.

Contig set

Merged set of Cj_nc_contigs and Ib_nc_contigs

Classification

Reads mapped onto C. japonica (%)a

Reads mapped onto I.balsamina (%)a

AUCb

Mapped reads

Number of reads (%)

0.981

Cj_nc_reads

76,775,986

2,712,459

(67.3)

(2.38)

Ib_nc_reads

195,363

71,599,224

(0.22)

(80.9)

B.

Contig set

Merged set of Cj_contigs_ci1 and Ib_contigs

Classification

Reads mapped onto C. japonica (%)a

Reads mapped onto I.balsamina (%)a

AUCb

Mapped reads

Number of reads (%)

0.995

Cj_nc_reads

73,819,654

442,526

(64.7)

(0.39)

Ib_nc_reads

271,929

71,471,262

(0.31)

(80.8)

C.

Contig set

Merged set of Cj_contigs_ci1 and Ib_contigs

Classification

Reads mapped onto C. japonica (%)a

Reads mapped onto I.balsamina (%)a

AUCb

Mapped reads

Number of reads (%)

0.995

Cj_nc_reads

58,501,463

324,744

(55.3)

(0.28)

Ib_nc_reads

197,487

60,709,899

(0.22)

(68.6)

  1. aNumbers indicate percentage of mapped reads to the total number of resds. bAUC; area under receiver operating characteristic (ROC) curve.
  2. Mapping parameter was as follows; In Panel A and Panel B, match length ≥90 bp and at most 1 mismatch and 1 gap allowed. In Panel C, match length =100 bp and no mismatch allowed.