Dog vs American black bear LastZ results
Dog (Canis lupus familiaris, ROS_Cfam_1.0) and American black bear (Ursus americanus, ASM334442v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 105. Dog 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) | 5000 |
| Threshold for gapped extension (L) | 5000 |
| Threshold for alignments between gapped alignment blocks (H) | 3000 |
| Masking count (M) | 10 |
| 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 | Dog | American black bear |
|---|---|---|
| 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 1,782,293 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Dog |
Uncovered: 400,585,553 out of 2,396,858,295 |
Uncovered: 431,669 out of 35,281,463 |
| American black bear |
Uncovered: 656,466,562 out of 2,588,393,916 |
Uncovered: 1,315,449 out of 29,000,040 |
Block size distribution
| Size range | All 1,782,293 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 58,993 |
365.4 kb |
|||
| 10 bp - 100 bp | 146,195 |
7.4 Mb |
19,217 |
1.3 Mb |
|
| 100 bp - 1 kb | 898,900 |
412.9 Mb |
66,383 |
22.3 Mb |
|
| 1 kb - 10 kb | 674,892 |
1.6 Gb |
26,369 |
83.2 Mb |
|
| 10 kb - 100 kb | 3,312 |
41.8 Mb |
12,605 |
520.9 Mb |
|
| 100 kb - 1 Mb | 1 |
128.6 kb |
6,406 |
1.4 Gb |
|
| 1 Mb - 10 Mb | 9 |
10.9 Mb |
|||