Chicken vs Common wall lizard LastZ results
Chicken (Gallus gallus, bGalGal1.mat.broiler.GRCg7b) and Common wall lizard (Podarcis muralis, PodMur_1.0) 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 | Common wall lizard |
|---|---|---|
| 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 265,119 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Chicken |
Uncovered: 968,418,038 out of 1,053,332,251 |
Uncovered: 6,725,343 out of 31,304,036 |
| Common wall lizard |
Uncovered: 1,426,386,192 out of 1,511,002,858 |
Uncovered: 14,929,387 out of 37,562,069 |
Block size distribution
| Size range | All 265,119 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 434 |
2.2 kb |
|||
| 10 bp - 100 bp | 19,139 |
1.4 Mb |
3,878 |
285.3 kb |
|
| 100 bp - 1 kb | 235,929 |
73.8 Mb |
44,927 |
16.2 Mb |
|
| 1 kb - 10 kb | 9,615 |
14.5 Mb |
8,063 |
20.6 Mb |
|
| 10 kb - 100 kb | 2 |
30.7 kb |
880 |
23.7 Mb |
|
| 100 kb - 1 Mb | 95 |
23.0 Mb |
|||
| 1 Mb - 10 Mb | 4 |
5.9 Mb |
|||