Anopheles gambiae vs Anopheles arabiensis LastZ Results

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Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles arabiensis (Anopheles arabiensis, AaraD1) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release 1502. Anopheles gambiae 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: 81,660

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

Uncovered: 59,039,827 out of 273,109,044
Covered: 214,069,217 out of 273,109,044

Uncovered: 284,395 out of 20,801,863
Matches: 20,208,056 out of 20,801,863
Mismatches: 284,367 out of 20,801,863
Insertions: 25,045 out of 20,801,863

Anopheles arabiensis

Uncovered: 47,061,739 out of 246,567,867
Covered: 199,506,128 out of 246,567,867

Uncovered: 183,748 out of 21,157,777
Matches: 20,646,723 out of 21,157,777
Mismatches: 297,921 out of 21,157,777
Insertions: 29,385 out of 21,157,777

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 gambiae Anopheles arabiensis
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}