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 Ensembl Metazoa release . 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: 193,123

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

Uncovered: 173,155,461 out of 281,378,673
Covered: 108,223,212 out of 281,378,673

Uncovered: 812,563 out of 22,369,942
Matches: 16,659,824 out of 22,369,942
Mismatches: 4,360,080 out of 22,369,942
Insertions: 537,475 out of 22,369,942

Anopheles farauti

Uncovered: 88,527,113 out of 183,103,254
Covered: 94,576,141 out of 183,103,254

Uncovered: 563,877 out of 20,347,302
Matches: 15,245,802 out of 20,347,302
Mismatches: 4,114,434 out of 20,347,302
Insertions: 423,189 out of 20,347,302

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}