Drosophila melanogaster vs Lucilia cuprina LastZ Results

Back to all analyses

Drosophila melanogaster (Drosophila melanogaster, BDGP6) and Lucilia cuprina (Lucilia cuprina, ASM118794v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release . Drosophila melanogaster 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: 56,848

Genome coverage (bp) Coding exon coverage (bp)
Drosophila melanogaster

Uncovered: 123,056,813 out of 143,725,995
Covered: 20,669,182 out of 143,725,995

Uncovered: 7,068,951 out of 22,848,419
Matches: 10,337,562 out of 22,848,419
Mismatches: 5,031,571 out of 22,848,419
Insertions: 410,335 out of 22,848,419

Lucilia cuprina

Uncovered: 412,792,807 out of 434,128,924
Covered: 21,336,117 out of 434,128,924

Uncovered: 7,879,930 out of 22,222,068
Matches: 9,350,344 out of 22,222,068
Mismatches: 4,501,839 out of 22,222,068
Insertions: 489,955 out of 22,222,068

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

Drosophila melanogaster Lucilia cuprina
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}