Lucilia cuprina vs Glossina brevipalpis LastZ Results

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Lucilia cuprina (Lucilia cuprina, ASM118794v1) and Glossina brevipalpis (Glossina brevipalpis, GbreI1) 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: 76,711

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

Uncovered: 398,521,565 out of 434,128,924
Covered: 35,607,359 out of 434,128,924

Uncovered: 4,691,104 out of 22,222,068
Matches: 12,172,257 out of 22,222,068
Mismatches: 4,741,080 out of 22,222,068
Insertions: 617,627 out of 22,222,068

Glossina brevipalpis

Uncovered: 281,588,227 out of 315,360,362
Covered: 33,772,135 out of 315,360,362

Uncovered: 3,411,211 out of 20,476,686
Matches: 12,030,781 out of 20,476,686
Mismatches: 4,610,011 out of 20,476,686
Insertions: 424,683 out of 20,476,686

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 brevipalpis
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}