Drosophila melanogaster vs Anopheles darlingi LastZ Results

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Drosophila melanogaster (Drosophila melanogaster, BDGP6) and Anopheles darlingi (Anopheles darlingi, AdarC3) 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: 37,619

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

Uncovered: 131,671,359 out of 143,725,995
Covered: 12,054,636 out of 143,725,995

Uncovered: 11,915,968 out of 22,883,909
Matches: 7,185,033 out of 22,883,909
Mismatches: 3,471,402 out of 22,883,909
Insertions: 311,506 out of 22,883,909

Anopheles darlingi

Uncovered: 125,045,262 out of 136,950,925
Covered: 11,905,663 out of 136,950,925

Uncovered: 8,474,980 out of 18,146,626
Matches: 6,303,621 out of 18,146,626
Mismatches: 3,041,482 out of 18,146,626
Insertions: 326,543 out of 18,146,626

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 Anopheles darlingi
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}