Chicken vs Goodes thornscrub tortoise LastZ results
Chicken (Gallus gallus, bGalGal1.mat.broiler.GRCg7b) and Goodes thornscrub tortoise (Gopherus evgoodei, rGopEvg1_v1.p) 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 | Goodes thornscrub tortoise |
|---|---|---|
| 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 535,801 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Chicken |
Uncovered: 716,559,895 out of 1,053,332,251 |
Uncovered: 4,505,194 out of 31,304,036 |
| Goodes thornscrub tortoise |
Uncovered: 1,950,705,375 out of 2,298,547,364 |
Uncovered: 7,358,478 out of 31,217,359 |
Block size distribution
| Size range | All 535,801 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 2,026 |
13.7 kb |
|||
| 10 bp - 100 bp | 28,019 |
1.7 Mb |
1,625 |
117.2 kb |
|
| 100 bp - 1 kb | 393,269 |
184.1 Mb |
11,185 |
4.2 Mb |
|
| 1 kb - 10 kb | 112,463 |
183.0 Mb |
3,087 |
7.6 Mb |
|
| 10 kb - 100 kb | 24 |
299.5 kb |
363 |
10.4 Mb |
|
| 100 kb - 1 Mb | 96 |
32.1 Mb |
|||
| 1 Mb - 10 Mb | 53 |
167.8 Mb |
|||
| 10 Mb - 100 Mb | 5 |
146.9 Mb |
|||