Mapping Metrics
Alignment Summary
| Metric | Value | % |
|---|---|---|
| Total input reads | 31,316,620 | |
| Mapped reads | 30,470,870 | 97.30 |
| Unmapped reads | 845,750 | 2.70 |
| Reads with MAPQ [40:inf) | 22,993,805 | 73.42 |
| Reads with MAPQ [30:40) | 1,581,504 | 5.05 |
| Reads with MAPQ [20:30) | 379,430 | 1.21 |
| Reads with MAPQ [10:20) | 2,324,300 | 7.42 |
| Reads with MAPQ [ 0:10) | 3,191,831 | 10.19 |
| Reads with MAPQ NA (Unmapped reads) | 845,750 | 2.70 |
| Reads with indel R1 | 611,282 | 2.01 |
| Total bases R1 | 2,830,385,807 | |
| Mapped bases R1 | 2,757,059,417 | |
| Soft-clipped bases R1 | 96,059,836 | 3.48 |
| Mismatched bases R1 | 10,627,285 | 0.39 |
| Mismatched bases R1 (excl. indels) | 9,581,206 | 0.35 |
| Q30 bases R1 | 2,593,472,774 | 91.63 |
| Total alignments | 34,014,990 | |
| Secondary alignments | 3,543,373 | |
| Supplementary (chimeric) alignments | 747 | |
| Estimated read length | 90.38 | |
| Bases in reference genome | 3,105,715,063 | |
| Average sequenced coverage over genome | 0.91 | |
| Estimated sample contamination | NA | |
| DRAGEN mapping rate [mil. reads/second] | 1.54 |
Summary per read group
Read group TCTTAAAG.1
| Metric | Value | % |
|---|---|---|
| Total reads in RG | 31,316,620 | |
| Mapped reads | 30,470,870 | 97.30 |
| Unmapped reads | 845,750 | 2.70 |
| Reads with MAPQ [40:inf) | 22,993,805 | 73.42 |
| Reads with MAPQ [30:40) | 1,581,504 | 5.05 |
| Reads with MAPQ [20:30) | 379,430 | 1.21 |
| Reads with MAPQ [10:20) | 2,324,300 | 7.42 |
| Reads with MAPQ [ 0:10) | 3,191,831 | 10.19 |
| Reads with MAPQ NA (Unmapped reads) | 845,750 | 2.70 |
| Reads with indel R1 | 611,282 | 2.01 |
| Total bases R1 | 2,830,385,807 | |
| Mapped bases R1 | 2,757,059,417 | |
| Soft-clipped bases R1 | 96,059,836 | 3.48 |
| Mismatched bases R1 | 10,627,285 | 0.39 |
| Mismatched bases R1 (excl. indels) | 9,581,206 | 0.35 |
| Q30 bases R1 | 2,593,472,774 | 91.63 |
| Total alignments | 34,014,990 | |
| Secondary alignments | 3,543,373 | |
| Supplementary (chimeric) alignments | 747 | |
| Estimated read length | 90.38 | |
| Average sequenced coverage over genome | 0.91 |