Chicken vs Chinese softshell turtle LastZ results
Chicken (Gallus gallus, bGalGal1.mat.broiler.GRCg7b) and Chinese softshell turtle (Pelodiscus sinensis, PelSin_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 | Chinese softshell turtle |
|---|---|---|
| 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 459,330 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Chicken |
Uncovered: 802,675,099 out of 1,053,332,251 |
Uncovered: 5,810,116 out of 31,304,036 |
| Chinese softshell turtle |
Uncovered: 1,949,898,250 out of 2,202,483,752 |
Uncovered: 6,861,058 out of 28,389,223 |
Block size distribution
| Size range | All 459,330 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 1,008 |
6.3 kb |
|||
| 10 bp - 100 bp | 26,146 |
1.7 Mb |
4,017 |
293.0 kb |
|
| 100 bp - 1 kb | 363,078 |
159.5 Mb |
27,274 |
10.6 Mb |
|
| 1 kb - 10 kb | 69,085 |
108.6 Mb |
8,141 |
21.1 Mb |
|
| 10 kb - 100 kb | 13 |
168.6 kb |
1,224 |
38.4 Mb |
|
| 100 kb - 1 Mb | 490 |
154.2 Mb |
|||
| 1 Mb - 10 Mb | 33 |
45.4 Mb |
|||