Anopheles gambiae vs Anopheles quadriannulatus LastZ Results

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Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles quadriannulatus (Anopheles quadriannulatus, AquaS1) 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: 123,720

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

Uncovered: 25,247,816 out of 281,378,673
Covered: 256,130,857 out of 281,378,673

Uncovered: 97,438 out of 22,369,942
Matches: 19,896,429 out of 22,369,942
Mismatches: 2,346,058 out of 22,369,942
Insertions: 30,017 out of 22,369,942

Anopheles quadriannulatus

Uncovered: 30,100,939 out of 283,828,998
Covered: 253,728,059 out of 283,828,998

Uncovered: 61,626 out of 21,196,160
Matches: 20,362,538 out of 21,196,160
Mismatches: 737,823 out of 21,196,160
Insertions: 34,173 out of 21,196,160

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 quadriannulatus
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}