Human vs Polar bear LastZ results
Human (Homo sapiens, GRCh38) and Polar bear (Ursus maritimus, UrsMar_1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 95. Human 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 |
| 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 | Human | Polar bear |
|---|---|---|
| Chunk size | 30,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 10,100,000 | |
| Masking options | {default_soft_masking => 1} | {default_soft_masking => 1} |
Statistics over 2,160,979 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Human |
Uncovered: 1,456,258,691 out of 3,099,750,718 |
Uncovered: 1,746,981 out of 38,571,754 |
| Polar bear |
Uncovered: 764,622,728 out of 2,301,379,344 |
Uncovered: 1,223,020 out of 29,143,224 |
Block size distribution
| Size range | All 2,160,979 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 81,122 |
541.0 kb |
|||
| 10 bp - 100 bp | 270,875 |
12.7 Mb |
18,911 |
1.3 Mb |
|
| 100 bp - 1 kb | 1,232,687 |
558.4 Mb |
59,498 |
21.3 Mb |
|
| 1 kb - 10 kb | 575,468 |
1.1 Gb |
19,070 |
48.0 Mb |
|
| 10 kb - 100 kb | 820 |
11.1 Mb |
1,683 |
40.7 Mb |
|
| 100 kb - 1 Mb | 7 |
817.1 kb |
216 |
76.0 Mb |
|
| 1 Mb - 10 Mb | 215 |
769.1 Mb |
|||
| 10 Mb - 100 Mb | 47 |
767.5 Mb |
|||