Chicken vs Zebra finch LastZ results
Chicken (Gallus gallus, bGalGal1.mat.broiler.GRCg7b) and Zebra finch (Taeniopygia guttata, bTaeGut1_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 | Zebra finch |
|---|---|---|
| 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 733,550 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Chicken |
Uncovered: 312,311,650 out of 1,053,332,251 |
Uncovered: 3,070,099 out of 31,304,036 |
| Zebra finch |
Uncovered: 316,993,407 out of 1,057,995,280 |
Uncovered: 4,602,954 out of 30,887,957 |
Block size distribution
| Size range | All 733,550 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 16,813 |
114.1 kb |
|||
| 10 bp - 100 bp | 65,395 |
3.0 Mb |
1,145 |
81.2 kb |
|
| 100 bp - 1 kb | 379,208 |
185.8 Mb |
5,642 |
1.9 Mb |
|
| 1 kb - 10 kb | 271,288 |
592.6 Mb |
1,542 |
4.2 Mb |
|
| 10 kb - 100 kb | 846 |
10.6 Mb |
224 |
7.0 Mb |
|
| 100 kb - 1 Mb | 109 |
43.4 Mb |
|||
| 1 Mb - 10 Mb | 72 |
245.7 Mb |
|||
| 10 Mb - 100 Mb | 16 |
489.8 Mb |
|||