Anopheles gambiae vs Anopheles darlingi LastZ Results

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Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles darlingi (Anopheles darlingi, AdarC3) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release 1506. Anopheles gambiae 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: 95,142

Genome coverage (bp) Coding exon coverage (bp)
Anopheles gambiae

Uncovered: 238,752,887 out of 273,109,044
Covered: 34,356,157 out of 273,109,044

Uncovered: 1,967,268 out of 20,801,863
Matches: 13,959,843 out of 20,801,863
Mismatches: 4,384,008 out of 20,801,863
Insertions: 490,744 out of 20,801,863

Anopheles darlingi

Uncovered: 104,194,727 out of 136,950,925
Covered: 32,756,198 out of 136,950,925

Uncovered: 1,488,986 out of 18,147,199
Matches: 12,343,932 out of 18,147,199
Mismatches: 3,775,074 out of 18,147,199
Insertions: 539,207 out of 18,147,199

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

Anopheles gambiae 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}