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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

ParameterValue
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

ParameterLucilia cuprinaStomoxys calcitrans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
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
Covered: 69,582,543 out of 434,128,924

Uncovered: 3,363,989 out of 22,222,068
Matches: 13,503,496 out of 22,222,068
Mismatches: 4,832,181 out of 22,222,068
Insertions: 522,402 out of 22,222,068
Identity over aligned base-pairs: 71.6%

Stomoxys calcitrans

Uncovered: 907,522,742 out of 971,188,624
Covered: 63,665,882 out of 971,188,624

Uncovered: 2,719,433 out of 23,712,588
Matches: 14,974,028 out of 23,712,588
Mismatches: 5,404,899 out of 23,712,588
Insertions: 614,228 out of 23,712,588
Identity over aligned base-pairs: 71.3%

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