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Table 5 The alignment rate and precision of Bowtie2 on single-end simulated data with different initial values of K.

From: Re-alignment of the unmapped reads with base quality score

  50-bp 75-bp 100-bp
K Align.Rate(%) Prec(%) Align.Rate(%) Prec(%) Align.Rate(%) Prec(%)
10 0.870362 0.981524 0.858727 0.981852 0.834774 0.981529
9 0.869464 0.981703 0.856311 0.982638 0.832754 0.982217
8 0.868262 0.982009 0.853695 0.983442 0.830495 0.982984
7 0.866564 0.982608 0.85074 0.984281 0.827873 0.983787
6 0.864261 0.983586 0.847368 0.985199 0.824662 0.984629
5 0.861039 0.985146 0.84329 0.98618 0.820193 0.985421
4 0.856596 0.987344 0.837615 0.987297 0.812949 0.986246
3 0.850384 0.990075 0.828366 0.988768 0.800774 0.987542
2 0.841539 0.993 0.813271 0.991168 0.782962 0.990233
1 0.825283 0.995516 0.794526 0.994829 0.763764 0.993865
  1. There are 7,740,912 simulated single-end reads with length 50-bp, 5,156,962 with length 75-bp, and 3,868,843 with length 100-bp.