Anopheles albimanus vs Anopheles christyi LastZ Results

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Anopheles albimanus (Anopheles albimanus, AalbS2) and Anopheles christyi (Anopheles christyi, AchrA1) 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: 93,766

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

Uncovered: 140,438,537 out of 173,339,240
Covered: 32,900,703 out of 173,339,240

Uncovered: 1,984,210 out of 20,837,397
Matches: 13,679,042 out of 20,837,397
Mismatches: 4,499,434 out of 20,837,397
Insertions: 674,711 out of 20,837,397

Anopheles christyi

Uncovered: 140,009,129 out of 172,658,580
Covered: 32,649,451 out of 172,658,580

Uncovered: 1,229,069 out of 17,808,626
Matches: 12,134,397 out of 17,808,626
Mismatches: 4,008,554 out of 17,808,626
Insertions: 436,606 out of 17,808,626

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 christyi
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}