Table 1.
Mapping statistics of the DLAF and dUTP RNA-seq libraries.
| Cell type | Direction of sequencing |
Replicate # |
Sample | Total reads, T (in millions) |
Total mapped reads, M (in millions) |
rRNA reads (as % of M) |
mtRNA reads (as % of M) |
Non-rRNA and non-mtRNA reads (as % of M) |
Reads with multiple alignments, nU (>1; in millions) |
Alignment rate (as percentage) |
Ratio DLAF/dUTP alignment rates |
||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Total, M/T |
Unique, [M-nU]/T |
Total | Unique | ||||||||||
| WT mESCs | Read 1 | 1 | dUTP_r1 | 59.68 | 31.33 | 9.9 | 3.7 | 86.4 | 8.24 | 52.5 | 38.7 | 1.219 (0.0355) | 1.352 (0.0675) |
| DLAF_r1 | 26.20 | 17.01 | 6.7 | 7.2 | 86.0 | 2.97 | 64.9 | 53.6 | |||||
| 2 | dUTP_r1 | 59.13 | 32.64 | 8.4 | 5.1 | 86.5 | 7.83 | 55.2 | 42.0 | ||||
| DLAF_r1 | 76.57 | 50.78 | 6.0 | 7.8 | 86.2 | 8.44 | 66.3 | 55.3 | |||||
| Read 2 | 1 | dUTP_r2 | 42.63 | 23.49 | 10.4 | 3.3 | 86.3 | 7.76 | 55.1 | 36.9 | 1.117 (0.0026) | 1.301 (0.0354) | |
| DLAF_r2 | 27.90 | 17.16 | 6.1 | 7.1 | 86.8 | 3.57 | 61.5 | 48.7 | |||||
| 2 | dUTP_r2 | 41.68 | 23.56 | 9.1 | 4.7 | 86.2 | 7.07 | 56.5 | 39.6 | ||||
| DLAF_r2 | 71.52 | 45.22 | 5.6 | 7.7 | 86.8 | 8.91 | 63.2 | 50.8 | |||||
|
Kdm1a-deficient mESCs |
Read 1 | 1 | dUTP_r1 | 61.01 | 26.55 | 14.0 | 1.7 | 84.3 | 11.04 | 43.5 | 25.4 | 1.275 (0.0044) | 1.540 (0.0060) |
| DLAF_r1 | 64.24 | 35.71 | 15.5 | 5.0 | 79.5 | 10.53 | 55.6 | 39.2 | |||||
| 2 | dUTP_r1 | 70.94 | 31.37 | 17.5 | 1.5 | 80.9 | 13.27 | 44.2 | 25.5 | ||||
| DLAF_r1 | 75.01 | 42.22 | 17.0 | 4.7 | 78.3 | 12.82 | 56.3 | 39.2 | |||||
| Read 2 | 1 | dUTP_r2 | 43.49 | 19.98 | 15.0 | 1.5 | 83.5 | 10.29 | 45.9 | 22.3 | 1.165 (0.0087) | 1.567 (0.0505) | |
| DLAF_r2 | 63.32 | 34.01 | 14.5 | 4.8 | 80.8 | 11.55 | 53.7 | 35.5 | |||||
| 2 | dUTP_r2 | 49.19 | 22.78 | 18.8 | 1.4 | 79.8 | 11.45 | 46.3 | 23.0 | ||||
| DLAF_r2 | 71.90 | 38.64 | 16.0 | 4.6 | 79.4 | 13.12 | 53.7 | 35.5 | |||||
DLAF, Direct Ligation of sequencing Adaptors to the First-strand cDNA; mES, mouse embryonic stem; WT, wild type.
Overall mappability (M/T) is calculated as the percentage of total number of reads (T) that map to the genome (M). Uniquely mapped reads (M–nU) are total mapped reads excluding the reads that map to multiple (non-unique) positions in the genome. Mean ratio and the range of data (in parentheses) are shown.