Anopheles melas vs Anopheles quadriannulatus LastZ Results

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Anopheles melas (Anopheles melas, AmelC2) and Anopheles quadriannulatus (Anopheles quadriannulatus, AquaS1) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release 1506. Anopheles melas 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: 79,652

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

Uncovered: 36,167,670 out of 224,162,116
Covered: 187,994,446 out of 224,162,116

Uncovered: 286,674 out of 20,488,804
Matches: 19,747,717 out of 20,488,804
Mismatches: 410,826 out of 20,488,804
Insertions: 43,587 out of 20,488,804

Anopheles quadriannulatus

Uncovered: 100,933,256 out of 283,828,998
Covered: 182,895,742 out of 283,828,998

Uncovered: 553,264 out of 20,971,893
Matches: 19,952,227 out of 20,971,893
Mismatches: 424,254 out of 20,971,893
Insertions: 42,148 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 melas 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}