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 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: 105,829

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

Uncovered: 25,370,195 out of 281,378,673
Covered: 256,008,478 out of 281,378,673

Uncovered: 89,969 out of 22,369,942
Matches: 21,166,434 out of 22,369,942
Mismatches: 1,086,946 out of 22,369,942
Insertions: 26,593 out of 22,369,942

Anopheles arabiensis

Uncovered: 20,344,042 out of 246,567,867
Covered: 226,223,825 out of 246,567,867

Uncovered: 78,835 out of 21,731,225
Matches: 20,864,666 out of 21,731,225
Mismatches: 759,189 out of 21,731,225
Insertions: 28,535 out of 21,731,225

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 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}