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 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: 86,064

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

Uncovered: 66,359,712 out of 273,109,044
Covered: 206,749,332 out of 273,109,044

Uncovered: 433,788 out of 20,801,863
Matches: 20,011,475 out of 20,801,863
Mismatches: 326,385 out of 20,801,863
Insertions: 30,215 out of 20,801,863

Anopheles quadriannulatus

Uncovered: 88,516,627 out of 283,828,998
Covered: 195,312,371 out of 283,828,998

Uncovered: 198,096 out of 20,971,893
Matches: 20,403,499 out of 20,971,893
Mismatches: 335,772 out of 20,971,893
Insertions: 34,526 out of 20,971,893

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 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}