Human vs Arctic ground squirrel LastZ results
Human (Homo sapiens, GRCh38) and Arctic ground squirrel (Urocitellus parryii, ASM342692v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 96. 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 |
| 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 | Human | Arctic ground squirrel |
|---|---|---|
| Chunk size | 30,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options | {default_soft_masking => 1} | {default_soft_masking => 1} |
Statistics over 2,128,310 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Human |
Uncovered: 1,519,138,032 out of 3,096,649,726 |
Uncovered: 1,023,900 out of 35,604,148 |
| Arctic ground squirrel |
Uncovered: 1,072,682,610 out of 2,520,505,282 |
Uncovered: 1,294,640 out of 31,635,636 |
Block size distribution
| Size range | All 2,128,310 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 68,913 |
462.6 kb |
|||
| 10 bp - 100 bp | 257,672 |
12.2 Mb |
15,645 |
1.1 Mb |
|
| 100 bp - 1 kb | 1,264,184 |
565.9 Mb |
60,654 |
21.9 Mb |
|
| 1 kb - 10 kb | 535,922 |
1.1 Gb |
23,050 |
62.7 Mb |
|
| 10 kb - 100 kb | 1,612 |
22.1 Mb |
2,795 |
66.0 Mb |
|
| 100 kb - 1 Mb | 7 |
767.2 kb |
602 |
237.6 Mb |
|
| 1 Mb - 10 Mb | 437 |
1.1 Gb |
|||
| 10 Mb - 100 Mb | 10 |
138.9 Mb |
|||