Table 1 Basic statistics produced by SA_Run2Ref for two sequencing run datasets.
From: SeqAssist: a novel toolkit for preliminary analysis of next-generation sequencing data
Illumina MiSeq runs (read length = 2 × 151 bp) | ECT | ECT_rerun | ECT + ECT_rerun |
|---|---|---|---|
Total number of raw paired-end reads | 7,575,822 | 7,064,035 | 14,639,857 |
Total number of cleaned reads | 7,524,261 | 7,041,454 | 14,565,715 |
Total number of reads mapped to reference genome | 6,573,572 | 6,193,164 | 12,766,736 |
Mapped/Cleaned reads (%) | 87.37 | 87.95 | 87.65 |
Total number of scaffolds in reference genome | 5,191 | 5,191 | 5,191 |
Number of covered reference scaffolds | 3,960 | 3,948 | 3,998 |
Covered/Total scaffolds (%) | 76.29 | 76.05 | 77.02 |
Genome coverage breadth (%) | 64.48 | 64.32 | 66.12 |
Genome coverage depth | 9.24 | 8.67 | 17.91 |
standard deviation of scaffold coverage depth | 96.11 | 91.88 | 186.95 |
average scaffold coverage depth | 16.27 | 15.41 | 31.33 |
Genome coverage evenness | 6.79 | 6.86 | 6.82 |
Run time (min) | 44.6 | 42.0 | 81.9 |