Sequencing | Mapping |
|---|
Breed | Raw reads | Paired l32q201 | Concordant2% | Neither end3% | One end4% | Diff chr5% | Too short6 | Too long7 | Relative orientation8 |
|---|
Brown egg layer
| 31.61 | 23.59 | 76.14 | 23.22 | 0.52 | 0.02 | 470 | 22547 | 549 |
White egg layer
| 29.70 | 21.84 | 73.30 | 25.81 | 0.64 | 0.14 | 1019 | 22058 | 1872 |
Broiler 1
| 34.82 | 24.83 | 78.26 | 21.14 | 0.48 | 0.01 | 2108 | 21209 | 335 |
Broiler 2
| 32.28 | 20.64 | 76.60 | 22.64 | 0.54 | 0.07 | 7388 | 22058 | 1030 |
- Paired-end sequencing of RRLs resulted in the indicated number of raw reads per breed. Sequencing read counts are in millions. Mapping percentages are relative to Paired l32q20.
- 1Paired l32q20 = paired reads had the RRL restriction tag trimmed to 32 bp and were filtered for a minimum per base quality of 20;
- 2Concordant = both reads of a read pair mapped to the expected orientation relative to each other and in the expected distance according to the RRL size range;
- 3Neither end = none of the reads of a read pair mapped to the reference;
- 4One end = only one read of a read pair was mapped;
- 5Diff chr = both reads of a read pair mapped, but to different chromosomes;
- 6Too short = both reads of a read pair mapped to the expected orientation relative to each other but at a closer distance than expected based on the RRL size range;
- 7Too long = both reads of a read pair mapped at a larger distance from each other than expected;
- 8Relative orientation = reads of a read pair mapped in another orientation relative to each other than expected based on the reference chicken genome.
