Anopheles gambiae vs Anopheles merus LastZ Results

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Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles merus (Anopheles merus, AmerM2) 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: 103,685

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

Uncovered: 63,147,626 out of 273,109,044
Covered: 209,961,418 out of 273,109,044

Uncovered: 310,020 out of 20,801,863
Matches: 20,007,531 out of 20,801,863
Mismatches: 446,401 out of 20,801,863
Insertions: 37,911 out of 20,801,863

Anopheles merus

Uncovered: 90,887,970 out of 288,048,996
Covered: 197,161,026 out of 288,048,996

Uncovered: 141,400 out of 19,203,252
Matches: 18,611,149 out of 19,203,252
Mismatches: 408,419 out of 19,203,252
Insertions: 42,284 out of 19,203,252

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 merus
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}