Lucilia cuprina vs Stomoxys calcitrans LastZ results
Lucilia cuprina (Lucilia cuprina, ASM118794v1) and Stomoxys calcitrans (Stomoxys calcitrans, ScalU1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release 99. Lucilia cuprina 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) | |
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 | Lucilia cuprina | Stomoxys calcitrans |
---|---|---|
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 191,465 alignment blocks
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Lucilia cuprina |
Uncovered: 364,546,381 out of 434,128,924 |
Uncovered: 3,363,989 out of 22,222,068 |
Stomoxys calcitrans |
Uncovered: 907,522,742 out of 971,188,624 |
Uncovered: 2,719,433 out of 23,712,588 |
Block size distribution
Size range | All 191,465 alignment blocks | Blocks grouped in nets | |||
---|---|---|---|---|---|
# blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
1 bp - 10 bp | 692 |
3.7 kb |
|||
10 bp - 100 bp | 32,525 |
2.2 Mb |
16,932 |
1.2 Mb |
|
100 bp - 1 kb | 134,382 |
46.9 Mb |
80,305 |
28.1 Mb |
|
1 kb - 10 kb | 23,838 |
48.0 Mb |
22,201 |
55.6 Mb |
|
10 kb - 100 kb | 28 |
326.9 kb |
686 |
12.3 Mb |
|
100 kb - 1 Mb | 1 |
102.6 kb |