Anopheles gambiae vs Anopheles albimanus LastZ Results

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Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles albimanus (Anopheles albimanus, AalbS2) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release 86. Anopheles gambiae 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: 111,731

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

Uncovered: 236,050,063 out of 273,109,044
Covered: 37,058,981 out of 273,109,044

Uncovered: 1,866,867 out of 21,204,221
Matches: 14,361,294 out of 21,204,221
Mismatches: 4,458,576 out of 21,204,221
Insertions: 517,484 out of 21,204,221

Anopheles albimanus

Uncovered: 138,204,629 out of 173,339,240
Covered: 35,134,611 out of 173,339,240

Uncovered: 1,724,267 out of 20,837,397
Matches: 14,061,345 out of 20,837,397
Mismatches: 4,376,084 out of 20,837,397
Insertions: 675,701 out of 20,837,397

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 gambiae Anopheles albimanus
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}