Cow vs Yarkand deer LastZ results
Cow (Bos taurus, ARS-UCD1.3) and Yarkand deer (Cervus hanglu yarkandensis, CEY_v1) 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 | Yarkand deer |
|---|---|---|
| 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 920,406 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Cow |
Uncovered: 452,142,019 out of 2,711,209,831 |
Uncovered: 1,374,148 out of 37,648,360 |
| Yarkand deer |
Uncovered: 392,191,502 out of 2,594,114,534 |
Uncovered: 2,512,516 out of 35,871,670 |
Block size distribution
| Size range | All 920,406 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 18,963 |
118.4 kb |
|||
| 10 bp - 100 bp | 69,839 |
3.6 Mb |
18,504 |
1.2 Mb |
|
| 100 bp - 1 kb | 292,639 |
135.0 Mb |
45,002 |
13.6 Mb |
|
| 1 kb - 10 kb | 508,281 |
1.7 Gb |
9,240 |
28.1 Mb |
|
| 10 kb - 100 kb | 30,680 |
440.8 Mb |
1,661 |
39.1 Mb |
|
| 100 kb - 1 Mb | 4 |
452.9 kb |
76 |
21.0 Mb |
|
| 1 Mb - 10 Mb | 11 |
48.2 Mb |
|||
| 10 Mb - 100 Mb | 36 |
2.0 Gb |
|||
| 100 Mb - 1 Gb | 1 |
101.2 Mb |
|||