Anopheles gambiae vs Anopheles stephensi LastZ Results

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Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles stephensi (Anopheles stephensi, AsteS1) 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: 193,232

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

Uncovered: 136,905,291 out of 273,109,044
Covered: 136,203,753 out of 273,109,044

Uncovered: 460,264 out of 20,801,863
Matches: 16,382,007 out of 20,801,863
Mismatches: 3,558,833 out of 20,801,863
Insertions: 400,759 out of 20,801,863

Anopheles stephensi

Uncovered: 99,223,226 out of 225,369,006
Covered: 126,145,780 out of 225,369,006

Uncovered: 435,234 out of 21,130,775
Matches: 16,652,585 out of 21,130,775
Mismatches: 3,662,591 out of 21,130,775
Insertions: 380,365 out of 21,130,775

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 stephensi
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}