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Table 4 SNPs called by GATK when using BWA or Bowtie2 (Bt2) to align Bs-1 reads against simulated contig assemblies

From: Positional bias in variant calls against draft reference assemblies

Assembly

Bt2 Total

Bt2 Pos k

BWA Total

BWA Pos k

Sim_allp

97,020

3

488,839

69

Sim_sga_m75

97,740

28

500,829

948

Sim_sga_m77

97,727

27

501,055

917

Sim_soap_K69

96,485

35

497,002

2016

Sim_soap_K71

96,003

44

497,486

2004

  1. Total columns show the total number of SNPs in any position while ‘Pos k’ columns show the number of SNPs at position k