Anopheles albimanus vs Anopheles epiroticus LastZ Results

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Anopheles albimanus (Anopheles albimanus, AalbS2) and Anopheles epiroticus (Anopheles epiroticus, AepiE1) 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: 103,205

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

Uncovered: 138,251,913 out of 173,339,240
Covered: 35,087,327 out of 173,339,240

Uncovered: 1,774,268 out of 20,837,397
Matches: 13,910,317 out of 20,837,397
Mismatches: 4,459,819 out of 20,837,397
Insertions: 692,993 out of 20,837,397

Anopheles epiroticus

Uncovered: 188,602,130 out of 223,486,714
Covered: 34,884,584 out of 223,486,714

Uncovered: 1,588,036 out of 20,274,816
Matches: 13,796,756 out of 20,274,816
Mismatches: 4,401,182 out of 20,274,816
Insertions: 488,842 out of 20,274,816

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 epiroticus
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}