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 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: 133,275

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

Uncovered: 24,924,687 out of 281,378,673
Covered: 256,453,986 out of 281,378,673

Uncovered: 79,826 out of 22,369,942
Matches: 20,184,031 out of 22,369,942
Mismatches: 2,067,401 out of 22,369,942
Insertions: 38,684 out of 22,369,942

Anopheles merus

Uncovered: 45,510,599 out of 288,048,996
Covered: 242,538,397 out of 288,048,996

Uncovered: 43,213 out of 19,643,623
Matches: 18,792,861 out of 19,643,623
Mismatches: 764,797 out of 19,643,623
Insertions: 42,752 out of 19,643,623

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 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}