Human vs Nile tilapia LastZ results
Human (Homo sapiens, GRCh38) and Nile tilapia (Oreochromis niloticus, O_niloticus_UMD_NMBU) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 99. 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 | Nile tilapia |
|---|---|---|
| Chunk size | 30,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 10,100,000 | |
| Masking options |
Statistics over 262,797 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Human |
Uncovered: 3,066,038,233 out of 3,099,750,718 |
Uncovered: 17,631,298 out of 38,571,754 |
| Nile tilapia |
Uncovered: 971,748,084 out of 1,005,681,550 |
Uncovered: 26,759,043 out of 51,713,280 |
Block size distribution
| Size range | All 262,797 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 1,697 |
7.4 kb |
|||
| 10 bp - 100 bp | 53,869 |
4.1 Mb |
16,272 |
1.2 Mb |
|
| 100 bp - 1 kb | 205,509 |
40.7 Mb |
84,312 |
25.4 Mb |
|
| 1 kb - 10 kb | 1,717 |
2.6 Mb |
9,967 |
19.6 Mb |
|
| 10 kb - 100 kb | 5 |
131.0 kb |
74 |
1.2 Mb |
|
| 100 kb - 1 Mb | 1 |
106.1 kb |
|||