Drosophila melanogaster vs Anopheles gambiae LastZ Results

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Drosophila melanogaster (Drosophila melanogaster, BDGP6) and Anopheles gambiae (Anopheles gambiae, AgamP4) 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: 40,112

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

Uncovered: 131,494,534 out of 143,725,995
Covered: 12,231,461 out of 143,725,995

Uncovered: 11,724,242 out of 22,883,909
Matches: 7,352,803 out of 22,883,909
Mismatches: 3,482,370 out of 22,883,909
Insertions: 324,494 out of 22,883,909

Anopheles gambiae

Uncovered: 260,642,910 out of 273,109,044
Covered: 12,466,134 out of 273,109,044

Uncovered: 9,946,609 out of 20,799,406
Matches: 7,114,857 out of 20,799,406
Mismatches: 3,377,500 out of 20,799,406
Insertions: 360,440 out of 20,799,406

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 gambiae
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}