Anopheles gambiae vs Anopheles sinensis LastZ Results

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Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles sinensis (Anopheles sinensis, AsinS2) 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: 165,905

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

Uncovered: 217,634,670 out of 273,109,044
Covered: 55,474,374 out of 273,109,044

Uncovered: 1,873,486 out of 20,801,863
Matches: 14,347,634 out of 20,801,863
Mismatches: 4,108,538 out of 20,801,863
Insertions: 472,205 out of 20,801,863

Anopheles sinensis

Uncovered: 322,104,667 out of 375,763,635
Covered: 53,658,968 out of 375,763,635

Uncovered: 1,169,273 out of 17,240,992
Matches: 12,162,227 out of 17,240,992
Mismatches: 3,484,935 out of 17,240,992
Insertions: 424,557 out of 17,240,992

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 sinensis
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}