Illustration from Scientific Research

Primer base quality masking schematic. Base qualities for read segments determined to originate from synthetic primer sequences are set to 0. Black lines indicate the sequenced fragment. Solid gray lines with ticks represent primers/directionality. Gray dotted lines represent reads off the input fragment. Readthrough coverage refers to coverage from adjacent PCR tiles, required to call variants that overlap primers. Solid colored circles represent SNPs, either true or false positive (error).

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