Japanese medaka HdrR vs Makobe Island cichlid LastZ results
Japanese medaka HdrR (Oryzias latipes, ASM223467v1) and Makobe Island cichlid (Pundamilia nyererei, PunNye1.0) 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 | Makobe Island 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 352,437 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Japanese medaka HdrR |
Uncovered: 566,194,302 out of 734,057,086 |
Uncovered: 5,795,861 out of 40,334,262 |
| Makobe Island cichlid |
Uncovered: 657,493,829 out of 830,133,247 |
Uncovered: 5,040,664 out of 35,984,801 |
Block size distribution
| Size range | All 352,437 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 1,226 |
7.3 kb |
|||
| 10 bp - 100 bp | 26,616 |
1.7 Mb |
2,498 |
181.8 kb |
|
| 100 bp - 1 kb | 280,790 |
110.3 Mb |
15,547 |
5.6 Mb |
|
| 1 kb - 10 kb | 43,681 |
71.8 Mb |
4,361 |
11.1 Mb |
|
| 10 kb - 100 kb | 124 |
2.1 Mb |
658 |
19.9 Mb |
|
| 100 kb - 1 Mb | 273 |
88.1 Mb |
|||
| 1 Mb - 10 Mb | 36 |
61.0 Mb |
|||