Japanese medaka HdrR vs Midas cichlid LastZ results
Japanese medaka HdrR (Oryzias latipes, ASM223467v1) and Midas cichlid (Amphilophus citrinellus, Midas_v5) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 94. Japanese medaka HdrR 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 |
| Masking count (M) | |
| 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 | Japanese medaka HdrR | Midas cichlid |
|---|---|---|
| Chunk size | 10,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options | {default_soft_masking => 1} | {default_soft_masking => 1} |
Statistics over 364,312 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Japanese medaka HdrR |
Uncovered: 563,905,764 out of 734,057,086 |
Uncovered: 5,598,869 out of 40,334,262 |
| Midas cichlid |
Uncovered: 668,416,812 out of 844,902,565 |
Uncovered: 5,037,842 out of 34,548,519 |
Block size distribution
| Size range | All 364,312 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 1,413 |
8.7 kb |
|||
| 10 bp - 100 bp | 27,377 |
1.7 Mb |
2,737 |
199.8 kb |
|
| 100 bp - 1 kb | 290,697 |
114.3 Mb |
16,517 |
5.9 Mb |
|
| 1 kb - 10 kb | 44,807 |
72.9 Mb |
4,862 |
12.3 Mb |
|
| 10 kb - 100 kb | 18 |
267.5 kb |
747 |
25.7 Mb |
|
| 100 kb - 1 Mb | 371 |
112.5 Mb |
|||
| 1 Mb - 10 Mb | 23 |
32.5 Mb |
|||