Chicken vs Eastern brown snake LastZ results
Chicken (Gallus gallus, bGalGal1.mat.broiler.GRCg7b) and Eastern brown snake (Pseudonaja textilis, EBS10Xv2-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 | Eastern brown 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 206,715 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Chicken |
Uncovered: 993,453,081 out of 1,053,332,251 |
Uncovered: 7,705,348 out of 31,304,036 |
| Eastern brown snake |
Uncovered: 1,531,593,025 out of 1,590,035,073 |
Uncovered: 7,841,787 out of 28,191,271 |
Block size distribution
| Size range | All 206,715 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 461 |
2.3 kb |
|||
| 10 bp - 100 bp | 17,940 |
1.3 Mb |
4,452 |
336.3 kb |
|
| 100 bp - 1 kb | 182,100 |
51.6 Mb |
48,772 |
16.7 Mb |
|
| 1 kb - 10 kb | 6,201 |
9.6 Mb |
8,202 |
21.4 Mb |
|
| 10 kb - 100 kb | 13 |
188.7 kb |
723 |
16.7 Mb |
|
| 100 kb - 1 Mb | 44 |
7.6 Mb |
|||