Lucilia cuprina vs Musca domestica LastZ Results

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Lucilia cuprina (Lucilia cuprina, ASM118794v1) and Musca domestica (Musca domestica, MdomA1) 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: 175,428

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

Uncovered: 373,771,772 out of 434,128,924
Covered: 60,357,152 out of 434,128,924

Uncovered: 3,341,305 out of 22,222,068
Matches: 13,545,679 out of 22,222,068
Mismatches: 4,811,506 out of 22,222,068
Insertions: 523,578 out of 22,222,068

Musca domestica

Uncovered: 678,698,562 out of 750,403,944
Covered: 71,705,382 out of 750,403,944

Uncovered: 2,443,862 out of 23,391,356
Matches: 14,992,809 out of 23,391,356
Mismatches: 5,295,817 out of 23,391,356
Insertions: 658,868 out of 23,391,356

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 Musca domestica
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}