Drosophila melanogaster vs Aedes aegypti LastZ Results

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Drosophila melanogaster (Drosophila melanogaster, BDGP6) and Aedes aegypti (Aedes aegypti, AaegL3) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release 78. 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: 46,931

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

Uncovered: 131,668,272 out of 143,725,995
Covered: 12,057,723 out of 143,725,995

Uncovered: 12,052,740 out of 22,883,909
Matches: 7,052,374 out of 22,883,909
Mismatches: 3,440,431 out of 22,883,909
Insertions: 338,364 out of 22,883,909

Aedes aegypti

Uncovered: 1,369,599,972 out of 1,383,974,186
Covered: 14,374,214 out of 1,383,974,186

Uncovered: 11,479,202 out of 22,623,919
Matches: 7,303,580 out of 22,623,919
Mismatches: 3,569,956 out of 22,623,919
Insertions: 271,181 out of 22,623,919

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 Aedes aegypti
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}