Figure 6
From: Efficient digest of high-throughput sequencing data in a reproducible report
Read mapping statistics. (A) Map quality thresholds. The majority of reads (~95%) have the best mapping score (mapq = 70) assigned by the alignment program, suggesting high confidence of mapping results. (B) Base-level mismatch information, where M = matched bases; I = inserted bases; D = deleted bases; and S = soft clipping bases due to mismatches. (C) Duplication mapping (multiple reads mapped to the same genomic location). The x-axis represents the number of reads sharing the same mapping locations and the y-axis represents the total number of such locations. (D) Insertion size. When the BAM file includes information about paired-end reads, bamchop also summarizes the distribution of the distance between the mapped locations of the read pairs, which is known as insertion size. Insertion size equals to the size of a DNA fragment in sequencing library to be sequenced in pair.