Table 2.
Overview of Mapping Status for embryonic days 16 and 19 bursal cells from Hy-Line W-36 embryos.
| Sample name | ED16–1 | ED16–2 | ED16–3 | ED19–4 | ED19–5 | ED19–6 |
|---|---|---|---|---|---|---|
| Total reads | 108,265,978 | 91,273,790 | 98,572,368 | 93,731,648 | 81,008,984 | 75,090,170 |
| Total mapped | 72,596,169 (67.05%) | 63,189,781 (69.23%) | 64,549,916 (65.48%) | 73,839,829 (78.78%) | 63,762,738 (78.71%) | 58,442,981 (77.83%) |
| Multiple mapped | 1,294,393 (1.2%) | 1,128,156 (1.24%) | 881,085 (0.89%) | 779,336 (0.83%) | 836,206 (1.03%) | 614,071 (0.82%) |
| Uniquely mapped | 71,301,776 (65.86%) | 62,061,625 (68%) | 63,668,831 (64.59%) | 73,060,493 (77.95%) | 62,926,532 (77.68%) | 57,828,910 (77.01%) |
| Reads map to “+” | 35,643,288 (32.92%) | 31,017,135 (33.98%) | 31,840,274 (32.3%) | 36,514,788 (38.96%) | 31,445,453 (38.82%) | 28,903,917 (38.49%) |
| Reads map to “–” | 35,658,488 (32.94%) | 31,044,490 (34.01%) | 31,828,557 (32.29%) | 36,545,705 (38.99%) | 31,481,079 (38.86%) | 28,924,993 (38.52%) |
| Non-splice reads | 38,260,637 (35.34%) | 33,575,763 (36.79%) | 33,505,632 (33.99%) | 41,264,205 (44.02%) | 34,804,685 (42.96%) | 31,734,121 (42.26%) |
| Splice reads | 33,041,139 (30.52%) | 28,485,862 (31.21%) | 30,163,199 (30.6%) | 31,796,288 (33.92%) | 28,121,847 (34.71%) | 26,094,789 (34.75%) |
Mapping Results Details:
1. Total number of filtered reads (Clean data).
2. Total number of reads that can be mapped to the reference genome. In general, this number should be larger than 70% when there is no contamination and the correct reference genome is chosen.
3. Number of reads that can be mapped to multiple sites in the reference genome. This number is usually less than 10% of the total.
4. Number of reads that can be uniquely mapped to the reference genome.
5. Number of reads that map to the positive strand (+) or the minus strand (–).
6. Splice reads can be segmented and mapped to 2 exons (also named junction reads), whereas non-splice reads can be mapped entirely to a single exon. The ratio of splice reads depends on the insert size used in the RNA-Seq experiments.