Lucilia cuprina vs Glossina palpalis LastZ Results

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Lucilia cuprina (Lucilia cuprina, ASM118794v1) and Glossina palpalis (Glossina palpalis gambiensis, GpapI1) 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: 87,438

Genome coverage (bp) Coding exon coverage (bp)
Lucilia cuprina

Uncovered: 398,160,433 out of 434,128,924
Covered: 35,968,491 out of 434,128,924

Uncovered: 4,804,220 out of 22,222,068
Matches: 11,981,902 out of 22,222,068
Mismatches: 4,829,422 out of 22,222,068
Insertions: 606,524 out of 22,222,068

Glossina palpalis gambiensis

Uncovered: 342,167,311 out of 380,104,241
Covered: 37,936,930 out of 380,104,241

Uncovered: 4,989,704 out of 24,086,735
Matches: 13,352,378 out of 24,086,735
Mismatches: 5,265,636 out of 24,086,735
Insertions: 479,017 out of 24,086,735

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 Glossina palpalis
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}