Dear All I use the same bam file for both samtools mpileup (text pileup output) and weeSAM (visualization) analysis. However, I found out the coverage is not the same. For instance, weeSAM showed super high coverage,~116,000X, between region 10,045-10,084 due to AT repeats as shown in the image here but it is not detected in samtools mpileup. The same region only showed ~3,000X read coverage in samtools mpileup. Any reason for such differences?
[image: weeSAM.png] Thanks! CC
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