Anopheles arabiensis vs Anopheles melas LastZ Results

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Anopheles arabiensis (Anopheles arabiensis, AaraD1) and Anopheles melas (Anopheles melas, AmelC2) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release 1506. 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: 77,168

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

Uncovered: 61,900,510 out of 246,567,867
Covered: 184,667,357 out of 246,567,867

Uncovered: 636,344 out of 21,157,777
Matches: 20,043,030 out of 21,157,777
Mismatches: 437,395 out of 21,157,777
Insertions: 41,008 out of 21,157,777

Anopheles melas

Uncovered: 33,527,239 out of 224,162,116
Covered: 190,634,877 out of 224,162,116

Uncovered: 207,861 out of 20,488,804
Matches: 19,817,205 out of 20,488,804
Mismatches: 419,486 out of 20,488,804
Insertions: 44,252 out of 20,488,804

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 melas
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}