Anopheles coluzzii vs Anopheles quadriannulatus LastZ Results

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Anopheles coluzzii (Anopheles coluzzii, AcolM1) and Anopheles quadriannulatus (Anopheles quadriannulatus, AquaS1) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release 1502. Anopheles coluzzii 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: 74,513

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

Uncovered: 39,538,943 out of 224,455,335
Covered: 184,916,392 out of 224,455,335

Uncovered: 613,467 out of 19,049,684
Matches: 18,106,641 out of 19,049,684
Mismatches: 299,391 out of 19,049,684
Insertions: 30,185 out of 19,049,684

Anopheles quadriannulatus

Uncovered: 98,706,332 out of 283,828,998
Covered: 185,122,666 out of 283,828,998

Uncovered: 1,421,555 out of 20,971,893
Matches: 19,178,789 out of 20,971,893
Mismatches: 328,277 out of 20,971,893
Insertions: 43,272 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 coluzzii 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}