Lucilia cuprina vs Glossina pallidipes LastZ Results

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Lucilia cuprina (Lucilia cuprina, ASM118794v1) and Glossina pallidipes (Glossina pallidipes, GpalI1) 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: 89,399

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

Uncovered: 398,060,105 out of 434,128,924
Covered: 36,068,819 out of 434,128,924

Uncovered: 4,703,821 out of 22,222,068
Matches: 12,157,023 out of 22,222,068
Mismatches: 4,748,247 out of 22,222,068
Insertions: 612,977 out of 22,222,068

Glossina pallidipes

Uncovered: 320,476,217 out of 357,332,231
Covered: 36,856,014 out of 357,332,231

Uncovered: 5,075,820 out of 22,910,370
Matches: 12,466,032 out of 22,910,370
Mismatches: 4,921,920 out of 22,910,370
Insertions: 446,598 out of 22,910,370

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 pallidipes
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}