Table 2 Quality control metrics of the raw read mapping and counting
Slide | A1-1 | A1-2 | B1-2 | |||
|---|---|---|---|---|---|---|
Platform | NextSeq 2000 | Genolab M | NextSeq 2000 | Genolab M | NextSeq 2000 | Genolab M |
Fraction Reads in Spots Under Tissue | 80.30% | 80.40% | 83.30% | 83.40% | 70.30% | 70.20% |
Mean Reads per Spot | 20,278 | 19,000 | 27,482 | 25,062 | 44,622 | 34,597 |
Mean Reads Under Tissue per Spot | 15,975 | 14,885 | 15,672 | 14,174 | 25,492 | 19,558 |
Median UMI Counts per Spot | 10,744 | 12,618 | 2,751 | 2,918 | 10,275 | 10,405 |
Median Genes per Spot | 4,565 | 5,034 | 1,647 | 1,736 | 3,866 | 3,930 |
Genes Detected | 16,736 | 16,852 | 16,441 | 16,532 | 16,779 | 16,767 |
Reads Mapped to Probe Set | 98.60% | 98.30% | 96.10% | 95.90% | 98.10% | 97.50% |
Reads Mapped Confidently to Probe Set | 97.50% | 97.30% | 60.80% | 60.30% | 70.90% | 70.50% |
Reads Mapped Confidently to the Filtered Probe Set | 73.30% | 74.20% | 44.80% | 45.50% | 55.10% | 55.50% |