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Table 1 Effects of the differences between BWA and Bowtie 2 alignments on the accuracy of variant calling in simulated data set

From: VariantMetaCaller: automated fusion of variant calling pipelines for quantitative, precision-based filtering

Difference between BWA and Bowtie 2 in terms of SNPs Indels
  Mean difference 95 % CI P-value Mean difference 95 % CI P-value
Maximum sensitivity of VariantMetaCaller 0.028 0.027−0.029 2.2×10−16 0.044 0.042−0.046 2.2×10−16
Precision at maximum sensitivity 0.009 0.007−0.01 2.2×10−16 0.039 0.025−0.053 8.6×10−7
AUPRC of VariantMetaCaller 0.028 0.027−0.029 2.2×10−16 0.042 0.040−0.044 2.2×10−16