Anopheles albimanus vs Anopheles arabiensis LastZ Results

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Anopheles albimanus (Anopheles albimanus, AalbS2) and Anopheles arabiensis (Anopheles arabiensis, AaraD1) 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: 105,543

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

Uncovered: 138,253,929 out of 173,339,240
Covered: 35,085,311 out of 173,339,240

Uncovered: 1,681,381 out of 20,837,397
Matches: 14,097,732 out of 20,837,397
Mismatches: 4,383,144 out of 20,837,397
Insertions: 675,140 out of 20,837,397

Anopheles arabiensis

Uncovered: 211,099,321 out of 246,567,867
Covered: 35,468,546 out of 246,567,867

Uncovered: 2,027,382 out of 21,202,768
Matches: 14,186,277 out of 21,202,768
Mismatches: 4,439,613 out of 21,202,768
Insertions: 549,496 out of 21,202,768

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 arabiensis
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}