Anopheles albimanus vs Anopheles darlingi LastZ Results

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Anopheles albimanus (Anopheles albimanus, AalbS2) and Anopheles darlingi (Anopheles darlingi, AdarC3) 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: 50,813

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

Uncovered: 47,539,089 out of 173,339,240
Covered: 125,800,151 out of 173,339,240

Uncovered: 432,110 out of 20,837,397
Matches: 18,164,971 out of 20,837,397
Mismatches: 2,034,992 out of 20,837,397
Insertions: 205,324 out of 20,837,397

Anopheles darlingi

Uncovered: 8,637,874 out of 136,950,925
Covered: 128,313,051 out of 136,950,925

Uncovered: 74,753 out of 18,158,941
Matches: 16,142,431 out of 18,158,941
Mismatches: 1,734,419 out of 18,158,941
Insertions: 207,338 out of 18,158,941

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 darlingi
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}