Chicken vs Mainland tiger snake LastZ results
Chicken (Gallus gallus, bGalGal1.mat.broiler.GRCg7b) and Mainland tiger snake (Notechis scutatus, TS10Xv2-PRI) 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 | Mainland tiger snake |
|---|---|---|
| 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 205,889 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Chicken |
Uncovered: 993,082,868 out of 1,053,332,251 |
Uncovered: 7,785,807 out of 31,304,036 |
| Mainland tiger snake |
Uncovered: 1,606,777,035 out of 1,665,525,958 |
Uncovered: 7,786,533 out of 26,728,429 |
Block size distribution
| Size range | All 205,889 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 483 |
2.4 kb |
|||
| 10 bp - 100 bp | 17,820 |
1.3 Mb |
4,708 |
357.6 kb |
|
| 100 bp - 1 kb | 181,264 |
51.4 Mb |
52,007 |
17.8 Mb |
|
| 1 kb - 10 kb | 6,291 |
9.8 Mb |
8,585 |
22.0 Mb |
|
| 10 kb - 100 kb | 31 |
464.0 kb |
711 |
16.1 Mb |
|
| 100 kb - 1 Mb | 42 |
6.7 Mb |
|||