Zebrafish vs Golden-line barbel LastZ results
Zebrafish (Danio rerio, GRCz11) and Golden-line barbel (Sinocyclocheilus grahami, SAMN03320097.WGS_v1.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 99. Zebrafish 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 | Zebrafish | Golden-line barbel |
|---|---|---|
| Chunk size | 10,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options |
Statistics over 1,410,254 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Zebrafish |
Uncovered: 1,009,478,108 out of 1,373,471,384 |
Uncovered: 2,137,830 out of 42,031,845 |
| Golden-line barbel |
Uncovered: 1,118,934,908 out of 1,750,287,761 |
Uncovered: 4,549,684 out of 69,134,296 |
Block size distribution
| Size range | All 1,410,254 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 11,742 |
65.0 kb |
|||
| 10 bp - 100 bp | 201,076 |
11.3 Mb |
52,021 |
3.5 Mb |
|
| 100 bp - 1 kb | 1,039,196 |
441.7 Mb |
166,865 |
56.3 Mb |
|
| 1 kb - 10 kb | 157,691 |
256.1 Mb |
33,010 |
85.6 Mb |
|
| 10 kb - 100 kb | 548 |
8.4 Mb |
3,228 |
88.0 Mb |
|
| 100 kb - 1 Mb | 1 |
135.1 kb |
1,092 |
344.9 Mb |
|
| 1 Mb - 10 Mb | 91 |
139.3 Mb |
|||