Anopheles albimanus vs Anopheles sinensis LastZ Results

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Anopheles albimanus (Anopheles albimanus, AalbS2) and Anopheles sinensis (Anopheles sinensis, AsinS2) 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: 109,315

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

Uncovered: 137,568,632 out of 173,339,240
Covered: 35,770,608 out of 173,339,240

Uncovered: 2,370,636 out of 20,837,397
Matches: 13,535,685 out of 20,837,397
Mismatches: 4,295,207 out of 20,837,397
Insertions: 635,869 out of 20,837,397

Anopheles sinensis

Uncovered: 339,288,531 out of 375,763,635
Covered: 36,475,104 out of 375,763,635

Uncovered: 1,708,328 out of 17,240,992
Matches: 11,498,477 out of 17,240,992
Mismatches: 3,618,032 out of 17,240,992
Insertions: 416,155 out of 17,240,992

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 sinensis
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}