Anopheles albimanus vs Anopheles farauti LastZ Results

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Anopheles albimanus (Anopheles albimanus, AalbS2) and Anopheles farauti (Anopheles farauti, AfarF2) 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: 105,479

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

Uncovered: 137,286,829 out of 173,339,240
Covered: 36,052,411 out of 173,339,240

Uncovered: 1,736,574 out of 20,837,397
Matches: 13,975,018 out of 20,837,397
Mismatches: 4,422,559 out of 20,837,397
Insertions: 703,246 out of 20,837,397

Anopheles farauti

Uncovered: 147,582,783 out of 183,103,254
Covered: 35,520,471 out of 183,103,254

Uncovered: 1,874,511 out of 20,229,039
Matches: 13,598,546 out of 20,229,039
Mismatches: 4,267,302 out of 20,229,039
Insertions: 488,680 out of 20,229,039

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 farauti
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}