Table 1 Sequencing and alignment statistics of the control-inoculated (C) and T. harzianum T22-inoculated (T) tomato root samples at 24, 48 and 72 h of interaction

From: Transcriptome reprogramming, epigenetic modifications and alternative splicing orchestrate the tomato root response to the beneficial fungus Trichoderma harzianum

Sample

Raw reads (no.)

High-quality reads (no.)

Reads aligned onto the S. lycopersicum genome (no.)

Reads aligned onto the T. harzianum genome (no.)

   

Total mapped

Uniquely mapped

Total mapped

Uniquely mapped

C24

57,069,524

46,879,826

44,354,968 (94.6%)

43,190,733 (97.4%)

3 (–)

–

C48

49,480,290

40,703,519

38,059,461 (93.5%)

37,101,879 (97.5%)

10 (–)

–

C72

46,114,872

37,277,990

35,376,200 (94.9%)

38,442,807 (98.2%)

7 (–)

–

T24

47,457,859

38,753,059

36,681,531 (94.7%)

35,789,320 (97.6%)

11,309 (0.54%)

11,299 (~100%)

T48

50,908,596

41,928,916

39,703,689 (94.7%)

38,720,180 (97.5%)

24,014 (1.05%)

23,974 (~100%)

T72

52,392,405

43,442,331

41,085,823 (94.6%)

39,996,180 (97.3%)

32,288 (1.40%)

32,238 (~100%)

  1. For each sample, percentages of uniquely mapped reads (onto tomato or fungus genomes) were calculated based on the corresponding 'Total mapped' values. For the alignment onto the T. harzianum genome, the subset including all unmapped reads onto the tomato genome was used as input data. The given values are the average of three biological replicates
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