Anopheles merus vs Anopheles quadriannulatus LastZ Results

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Anopheles merus (Anopheles merus, AmerM2) and Anopheles quadriannulatus (Anopheles quadriannulatus, AquaS1) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release 1506. Anopheles merus 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: 80,624

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

Uncovered: 95,333,135 out of 288,048,996
Covered: 192,715,861 out of 288,048,996

Uncovered: 184,733 out of 19,203,252
Matches: 18,590,524 out of 19,203,252
Mismatches: 387,819 out of 19,203,252
Insertions: 40,176 out of 19,203,252

Anopheles quadriannulatus

Uncovered: 91,868,884 out of 283,828,998
Covered: 191,960,114 out of 283,828,998

Uncovered: 173,487 out of 20,971,893
Matches: 20,317,247 out of 20,971,893
Mismatches: 437,823 out of 20,971,893
Insertions: 43,336 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 merus 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}