Anopheles arabiensis vs Anopheles coluzzii LastZ Results

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Anopheles arabiensis (Anopheles arabiensis, AaraD1) and Anopheles coluzzii (Anopheles coluzzii, AcolM1) 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: 63,117

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

Uncovered: 57,997,994 out of 246,567,867
Covered: 188,569,873 out of 246,567,867

Uncovered: 1,450,184 out of 21,157,777
Matches: 19,390,205 out of 21,157,777
Mismatches: 280,236 out of 21,157,777
Insertions: 37,152 out of 21,157,777

Anopheles coluzzii

Uncovered: 34,929,440 out of 224,455,335
Covered: 189,525,895 out of 224,455,335

Uncovered: 497,096 out of 19,049,684
Matches: 18,279,947 out of 19,049,684
Mismatches: 249,296 out of 19,049,684
Insertions: 23,345 out of 19,049,684

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 coluzzii
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}