Human vs Pika LastZ results
Human (Homo sapiens, GRCh38) and Pika (Ochotona princeps, OchPri2.0-Ens) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 76. 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 | Pika |
|---|---|---|
| Chunk size | 30,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 10,100,000 | |
| Masking options | {default_soft_masking => 1} |
Statistics over 1,339,006 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Human |
Uncovered: 2,258,087,149 out of 3,099,750,718 |
Uncovered: 6,603,466 out of 38,571,754 |
| Pika |
Uncovered: 4,016,619,618 out of 4,781,903,803 |
Uncovered: 6,449,875 out of 26,511,260 |
Block size distribution
| Size range | All 1,339,006 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 13,454 |
89.7 kb |
|||
| 10 bp - 100 bp | 120,767 |
7.1 Mb |
15,141 |
1.1 Mb |
|
| 100 bp - 1 kb | 929,908 |
421.0 Mb |
103,940 |
45.8 Mb |
|
| 1 kb - 10 kb | 274,834 |
449.5 Mb |
67,401 |
181.2 Mb |
|
| 10 kb - 100 kb | 43 |
516.0 kb |
7,963 |
252.7 Mb |
|
| 100 kb - 1 Mb | 1,816 |
390.2 Mb |
|||
| 1 Mb - 10 Mb | 6 |
7.3 Mb |
|||