Table 7.
Basic QC analysis of WGS data. Basic QC and mapping quality summary statistics for both the cell lines computed using samtools and Samstat
| QC anlysis Summary | LiPSC-ER2.2 | LiPSC-GR1.1 |
|---|---|---|
| Total reads | 840146878 | 898394686 |
| Total reads mapped | 33656253 | 768473456 |
| Mean depth | 34.49 | 30.83 |
| deduplicated reads | 90375272 | 157504614 |
| Total reads after removing duplicates (%) | 749771606 (89.2 %) | 740890072 (82.5 %) |
| Reads mapped to human genome | 693727158 | 613291081 |
| MAPQ > =30 | 86.9 % | 79.6 % |
| MAPQ <30 | 0.1 % | 0.0 % |
| MAPQ <20 | 0.5 % | 0.5 % |
| MAPQ <10 | 0.7 % | 0.7 % |
| MAPQ <3 | 0.3 % | 0.3 % |