Anopheles gambiae vs Anopheles farauti LastZ Results

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Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles farauti (Anopheles farauti, AfarF2) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release 1506. 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: 189,452

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

Uncovered: 170,800,136 out of 273,109,044
Covered: 102,308,908 out of 273,109,044

Uncovered: 676,310 out of 20,801,863
Matches: 15,789,352 out of 20,801,863
Mismatches: 3,858,497 out of 20,801,863
Insertions: 477,704 out of 20,801,863

Anopheles farauti

Uncovered: 90,735,154 out of 183,103,254
Covered: 92,368,100 out of 183,103,254

Uncovered: 625,795 out of 20,229,039
Matches: 15,405,667 out of 20,229,039
Mismatches: 3,767,823 out of 20,229,039
Insertions: 429,754 out of 20,229,039

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

Chunking parameters

Anopheles gambiae Anopheles farauti
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}