Human vs Northern American deer mouse LastZ results
Human (Homo sapiens, GRCh38) and Northern American deer mouse (Peromyscus maniculatus bairdii, HU_Pman_2.1) 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 |
| 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 | Northern American deer mouse |
|---|---|---|
| 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 1,716,609 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Human |
Uncovered: 1,969,341,704 out of 3,099,750,718 |
Uncovered: 2,396,933 out of 38,571,754 |
| Northern American deer mouse |
Uncovered: 1,480,301,667 out of 2,512,423,440 |
Uncovered: 2,913,763 out of 33,606,407 |
Block size distribution
| Size range | All 1,716,609 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 30,851 |
209.2 kb |
|||
| 10 bp - 100 bp | 165,933 |
8.5 Mb |
10,228 |
714.3 kb |
|
| 100 bp - 1 kb | 1,128,634 |
522.4 Mb |
46,580 |
17.7 Mb |
|
| 1 kb - 10 kb | 390,805 |
680.9 Mb |
16,724 |
41.0 Mb |
|
| 10 kb - 100 kb | 384 |
5.5 Mb |
1,359 |
34.1 Mb |
|
| 100 kb - 1 Mb | 2 |
237.4 kb |
261 |
89.4 Mb |
|
| 1 Mb - 10 Mb | 132 |
487.7 Mb |
|||
| 10 Mb - 100 Mb | 29 |
547.1 Mb |
|||