Anopheles albimanus vs Anopheles quadriannulatus LastZ Results

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Anopheles albimanus (Anopheles albimanus, AalbS2) and Anopheles quadriannulatus (Anopheles quadriannulatus, AquaS1) 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: 104,158

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

Uncovered: 138,600,510 out of 173,339,240
Covered: 34,738,730 out of 173,339,240

Uncovered: 1,748,696 out of 20,837,397
Matches: 14,053,359 out of 20,837,397
Mismatches: 4,361,063 out of 20,837,397
Insertions: 674,279 out of 20,837,397

Anopheles quadriannulatus

Uncovered: 248,788,732 out of 283,828,998
Covered: 35,040,266 out of 283,828,998

Uncovered: 1,956,230 out of 21,002,255
Matches: 14,095,495 out of 21,002,255
Mismatches: 4,396,691 out of 21,002,255
Insertions: 553,839 out of 21,002,255

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 quadriannulatus
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}