Cow vs Hybrid - Bos Indicus LastZ results
Cow (Bos taurus, ARS-UCD1.3) and Hybrid - Bos Indicus (Bos indicus x Bos taurus, UOA_Brahman_1) 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 | Hybrid - Bos Indicus |
|---|---|---|
| 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 59,119 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Cow |
Uncovered: 74,966,668 out of 2,711,209,831 |
Uncovered: 150,581 out of 37,648,360 |
| Hybrid - Bos Indicus |
Uncovered: 75,869,027 out of 2,680,953,056 |
Uncovered: 596,997 out of 37,484,807 |
Block size distribution
| Size range | All 59,119 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 737 |
4.5 kb |
|||
| 10 bp - 100 bp | 6,214 |
311.4 kb |
1,830 |
108.4 kb |
|
| 100 bp - 1 kb | 11,753 |
4.5 Mb |
4,301 |
1.5 Mb |
|
| 1 kb - 10 kb | 11,443 |
47.6 Mb |
1,953 |
6.3 Mb |
|
| 10 kb - 100 kb | 20,548 |
858.1 Mb |
718 |
21.3 Mb |
|
| 100 kb - 1 Mb | 8,417 |
1.7 Gb |
80 |
19.1 Mb |
|
| 1 Mb - 10 Mb | 7 |
7.7 Mb |
4 |
19.4 Mb |
|
| 10 Mb - 100 Mb | 19 |
1.2 Gb |
|||
| 100 Mb - 1 Gb | 11 |
1.3 Gb |
|||