Anopheles arabiensis vs Anopheles quadriannulatus LastZ Results

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Anopheles arabiensis (Anopheles arabiensis, AaraD1) and Anopheles quadriannulatus (Anopheles quadriannulatus, AquaS1) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release 1502. Anopheles arabiensis 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: 68,100

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

Uncovered: 52,526,269 out of 246,567,867
Covered: 194,041,598 out of 246,567,867

Uncovered: 322,778 out of 21,157,777
Matches: 20,461,566 out of 21,157,777
Mismatches: 342,196 out of 21,157,777
Insertions: 31,237 out of 21,157,777

Anopheles quadriannulatus

Uncovered: 89,005,919 out of 283,828,998
Covered: 194,823,079 out of 283,828,998

Uncovered: 161,622 out of 20,971,893
Matches: 20,439,926 out of 20,971,893
Mismatches: 337,292 out of 20,971,893
Insertions: 33,053 out of 20,971,893

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 --identity=80..100 --matchcount=1000

Chunking parameters

Anopheles arabiensis Anopheles quadriannulatus
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}