Human vs Indian cobra LastZ results
Human (Homo sapiens, GRCh38) and Indian cobra (Naja naja, Nana_v5) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 101. 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 | Indian cobra |
|---|---|---|
| Chunk size | 30,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 10,100,000 | |
| Masking options |
Statistics over 290,748 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Human |
Uncovered: 3,026,625,817 out of 3,099,750,718 |
Uncovered: 12,202,787 out of 38,571,754 |
| Indian cobra |
Uncovered: 1,714,180,220 out of 1,768,535,092 |
Uncovered: 5,208,221 out of 27,810,543 |
Block size distribution
| Size range | All 290,748 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 932 |
4.3 kb |
|||
| 10 bp - 100 bp | 44,089 |
3.3 Mb |
15,849 |
1.2 Mb |
|
| 100 bp - 1 kb | 239,182 |
59.5 Mb |
108,989 |
35.6 Mb |
|
| 1 kb - 10 kb | 5,995 |
9.3 Mb |
13,520 |
29.0 Mb |
|
| 10 kb - 100 kb | 547 |
14.6 Mb |
644 |
20.0 Mb |
|
| 100 kb - 1 Mb | 3 |
374.7 kb |
10 |
1.4 Mb |
|