Drosophila melanogaster vs Drosophila sechellia LastZ Results

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Drosophila melanogaster (Drosophila melanogaster, BDGP6) and Drosophila sechellia (Drosophila sechellia, dsec_caf1) 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: 82,080

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

Uncovered: 25,629,271 out of 143,725,995
Covered: 118,096,724 out of 143,725,995

Uncovered: 346,471 out of 22,883,909
Matches: 21,523,484 out of 22,883,909
Mismatches: 934,695 out of 22,883,909
Insertions: 79,259 out of 22,883,909

Drosophila sechellia

Uncovered: 44,005,690 out of 166,577,145
Covered: 122,571,455 out of 166,577,145

Uncovered: 145,873 out of 21,488,559
Matches: 20,431,562 out of 21,488,559
Mismatches: 852,165 out of 21,488,559
Insertions: 58,959 out of 21,488,559

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 Drosophila sechellia
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}