Cow vs Wild yak LastZ results
Cow (Bos taurus, ARS-UCD1.3) and Wild yak (Bos mutus, BosGru_v2.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 111. Cow 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 | Cow | Wild yak |
|---|---|---|
| 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 277,951 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Cow |
Uncovered: 115,953,100 out of 2,711,209,831 |
Uncovered: 319,925 out of 37,648,360 |
| Wild yak |
Uncovered: 95,292,202 out of 2,645,161,911 |
Uncovered: 431,834 out of 32,081,175 |
Block size distribution
| Size range | All 277,951 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 2,169 |
13.5 kb |
|||
| 10 bp - 100 bp | 19,229 |
1.0 Mb |
5,701 |
341.4 kb |
|
| 100 bp - 1 kb | 54,679 |
23.6 Mb |
16,313 |
6.2 Mb |
|
| 1 kb - 10 kb | 117,246 |
519.7 Mb |
6,294 |
18.6 Mb |
|
| 10 kb - 100 kb | 84,279 |
2.0 Gb |
2,189 |
75.4 Mb |
|
| 100 kb - 1 Mb | 349 |
41.8 Mb |
2,154 |
907.0 Mb |
|
| 1 Mb - 10 Mb | 838 |
1.6 Gb |
|||