Lucilia cuprina vs Glossina austeni LastZ Results

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Lucilia cuprina (Lucilia cuprina, ASM118794v1) and Glossina austeni (Glossina austeni, GausT1) 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: 88,816

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

Uncovered: 397,882,988 out of 434,128,924
Covered: 36,245,936 out of 434,128,924

Uncovered: 4,763,849 out of 22,222,068
Matches: 12,098,365 out of 22,222,068
Mismatches: 4,751,912 out of 22,222,068
Insertions: 607,942 out of 22,222,068

Glossina austeni

Uncovered: 333,334,520 out of 370,264,922
Covered: 36,930,402 out of 370,264,922

Uncovered: 5,507,030 out of 23,999,935
Matches: 12,900,348 out of 23,999,935
Mismatches: 5,121,307 out of 23,999,935
Insertions: 471,250 out of 23,999,935

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 austeni
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}