Anopheles albimanus vs Anopheles merus LastZ Results

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Anopheles albimanus (Anopheles albimanus, AalbS2) and Anopheles merus (Anopheles merus, AmerM2) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release . Anopheles albimanus 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: 104,906

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

Uncovered: 138,349,626 out of 173,339,240
Covered: 34,989,614 out of 173,339,240

Uncovered: 1,673,332 out of 20,837,397
Matches: 14,098,091 out of 20,837,397
Mismatches: 4,389,549 out of 20,837,397
Insertions: 676,425 out of 20,837,397

Anopheles merus

Uncovered: 252,612,918 out of 288,048,996
Covered: 35,436,078 out of 288,048,996

Uncovered: 1,732,625 out of 19,263,672
Matches: 13,032,858 out of 19,263,672
Mismatches: 4,004,849 out of 19,263,672
Insertions: 493,340 out of 19,263,672

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 albimanus 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}