From: Long-read individual-molecule sequencing reveals CRISPR-induced genetic heterogeneity in human ESCs
Gene | Mutant allele frequency (%) / Type | Amplicon size | Sequencing platform | Read count | Reads with UMI | UMI groups for variant calling (≥ 5 reads) | Median read number per UMI group | UMI groups with introduced mutation | Somatic SNV count | Somatic SNV load per megabase | SV groups |
---|---|---|---|---|---|---|---|---|---|---|---|
EPOR | 1:100 (1%) | 168 bp | Nanopore | 17,634 | 6444 | 284 | 7 | 2 (0.7%) | 0 | N/A | N/A |
EPOR | 1:1000 (0.1%) | 6789 bp | PacBio | 227,206 | 136,399 | 3184 | 6 | 4 (0.126%) | 192 | 9.0 | 3 |
EPOR | 1:10,000 (0.01%) | 168 bp | Nanopore | 1,093,683 | 494,009 | 15,598 | 8 | 1 (0.006%) | 10 | 7.1 | N/A |
EPOR | 1:10,000 (0.01%) | 168 bp | Illumina | 7,488,257 | 7,236,007 | 132,341 | 7 | 5 (0.004%) | 85 | 7.1 | N/A |
PANX1 (Pan1) | WT | 7077 bp | Nanopore | 576,583 | 165,628 | 2810 | 6 | N/A | 73 | 3.8 | 0 |
PANX1 (Pan3) | WT | 6595 bp | Nanopore | 389,726 | 133,215 | 3867 | 7 | N/A | 103 | 4.1 | 0 |
PANX1 (Pan1) | Cas9 editing | 7077 bp | Nanopore | 2,761,805 | 613,147 | 3479 | 7 | N/A | 275 | 11.3 | 189 (5.4%) |
PANX1 (Pan3) | Cas9 editing | 6595 bp | Nanopore | 3,078,165 | 1,042,582 | 7281 | 10 | N/A | 624 | 13.1 | 204 (2.8%) |