Lucilia cuprina vs Stomoxys calcitrans LastZ Results

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Lucilia cuprina (Lucilia cuprina, ASM118794v1) and Stomoxys calcitrans (Stomoxys calcitrans, ScalU1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release . Lucilia cuprina was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 191,465

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

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

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
Other parameters (other)--ambiguous=iupac

Chunking parameters

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}