Anopheles arabiensis vs Anopheles merus LastZ Results

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Anopheles arabiensis (Anopheles arabiensis, AaraD1) and Anopheles merus (Anopheles merus, AmerM2) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release 1506. Anopheles arabiensis 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: 80,030

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

Uncovered: 52,272,950 out of 246,567,867
Covered: 194,294,917 out of 246,567,867

Uncovered: 194,389 out of 21,157,777
Matches: 20,453,561 out of 21,157,777
Mismatches: 466,876 out of 21,157,777
Insertions: 42,951 out of 21,157,777

Anopheles merus

Uncovered: 91,945,703 out of 288,048,996
Covered: 196,103,293 out of 288,048,996

Uncovered: 102,484 out of 19,203,252
Matches: 18,650,176 out of 19,203,252
Mismatches: 409,015 out of 19,203,252
Insertions: 41,577 out of 19,203,252

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 --identity=80..100 --matchcount=1000

Chunking parameters

Anopheles arabiensis Anopheles merus
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}