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Table 4 Alignment evaluation on simulated & real SNPs

From: UASIS: Universal Automatic SNP Identification System

  Simulated SNPs Real SNPs
Program Reads Time (s) Accuracy (%) Reads Time (s) Accuracy (%)
Bowtie-35 24326 2 76.4 72241 4 90.5
BWA-35 24326 5 83.4 72241 8 90.2
Bowtie-76 24359 3 89.2 72241 4 93.4
BWA-76 24359 9 92.8 72241 19 92.8
Bowtie-128 24373 2 90.1 72241 5 92.4
BWA-128 24373 5 94.7 72241 49 93.4
Bowtie-512 24373 3 93.8 72241 9 93.5
BWA-512 24373 23 97.2 72241 132 91.7
  1. Totally 94771 reads of 35, 76, 128 and 512bp were simulated from human genome build 37.1 with error rates following Sanger sequencing pattern. Such that for each read, average amount of mismatches and indels is 1 and 0.02. CPU time on a quad core of a 2.4 GHz Xeon E5620 processor with 8G RAM and accuracy in percentage are given.