Analysis Output | Sample Summary Reports | Tumor Sample Summary | Alignment Summary

Alignment Summary

Table 8 Alignment Summary
Statistic	Definition
Number of Reads	Total number of reads passing filter for this sample.
Coverage	Total number of aligned bases divided by the genome size.
Percent Duplicate Paired Reads	Percentage of paired reads that have duplicates.
Fragment Length Median	Median length of the sequenced fragment. The fragment length is calculated based on the locations at which a read pair aligns to the reference. The read mapping information is parsed from the BAM files.
Fragment Length Standard Deviation	Standard deviation of the sequenced fragment length.

Table 9 Read Statistics
Statistic	Definition
Percent Aligned	The percentage of reads passing filter that aligned to the reference genome.
Percent Q30	The percentage of bases with a quality score of 30 or higher.
Mismatch Rate	The average percentage of mismatches across both reads 1 and 2 over all cycles.