Human vs Abingdon island giant tortoise LastZ results
Human (Homo sapiens, GRCh38) and Abingdon island giant tortoise (Chelonoidis abingdonii, ASM359739v1) 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 | Abingdon island giant tortoise |
|---|---|---|
| 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 346,822 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Human |
Uncovered: 2,989,778,877 out of 3,099,750,718 |
Uncovered: 9,281,605 out of 38,571,754 |
| Abingdon island giant tortoise |
Uncovered: 2,208,152,769 out of 2,300,739,315 |
Uncovered: 6,391,783 out of 29,396,458 |
Block size distribution
| Size range | All 346,822 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 773 |
3.9 kb |
|||
| 10 bp - 100 bp | 39,029 |
2.9 Mb |
13,004 |
972.2 kb |
|
| 100 bp - 1 kb | 291,916 |
87.2 Mb |
120,687 |
43.3 Mb |
|
| 1 kb - 10 kb | 15,032 |
24.1 Mb |
20,335 |
46.4 Mb |
|
| 10 kb - 100 kb | 72 |
1.3 Mb |
863 |
19.4 Mb |
|
| 100 kb - 1 Mb | 35 |
5.4 Mb |
|||