Chicken vs Japanese quail LastZ results
Chicken (Gallus gallus, bGalGal1.mat.broiler.GRCg7b) and Japanese quail (Coturnix japonica, Coturnix_japonica_2.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 107. Chicken was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.
Configuration parameters
| Parameter | Value |
|---|---|
| Gap open penalty (O) | 400 |
| Gap extend penalty (E) | 30 |
| HSP threshold (K) | 3000 |
| Threshold for gapped extension (L) | 3000 |
| Threshold for alignments between gapped alignment blocks (H) | 2200 |
| Masking count (M) | |
| Seed and Transition value (T) | 1 |
| Scoring matrix (Q) | Default:
A C G T
91 -114 -31 -123
-114 100 -125 -31
-31 -125 100 -114
-123 -31 -114 91
|
Chunking parameters
| Parameter | Chicken | Japanese quail |
|---|---|---|
| Chunk size | 10,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 10,100,000 | 10,100,000 |
| Masking options |
Statistics over 395,618 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Chicken |
Uncovered: 192,189,853 out of 1,053,332,251 |
Uncovered: 1,881,419 out of 31,304,036 |
| Japanese quail |
Uncovered: 78,639,939 out of 927,656,957 |
Uncovered: 802,457 out of 27,520,960 |
Block size distribution
| Size range | All 395,618 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 10,263 |
67.3 kb |
|||
| 10 bp - 100 bp | 31,623 |
1.6 Mb |
3,113 |
205.5 kb |
|
| 100 bp - 1 kb | 138,277 |
65.9 Mb |
7,576 |
2.4 Mb |
|
| 1 kb - 10 kb | 204,245 |
647.2 Mb |
1,697 |
4.7 Mb |
|
| 10 kb - 100 kb | 11,210 |
162.5 Mb |
211 |
5.2 Mb |
|
| 100 kb - 1 Mb | 29 |
10.3 Mb |
|||
| 1 Mb - 10 Mb | 34 |
142.0 Mb |
|||
| 10 Mb - 100 Mb | 16 |
560.0 Mb |
|||
| 100 Mb - 1 Gb | 1 |
152.5 Mb |
|||