Anopheles melas vs Anopheles merus LastZ Results

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Anopheles melas (Anopheles melas, AmelC2) and Anopheles merus (Anopheles merus, AmerM2) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release 1506. Anopheles melas 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: 86,662

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

Uncovered: 34,827,810 out of 224,162,116
Covered: 189,334,306 out of 224,162,116

Uncovered: 219,183 out of 20,488,804
Matches: 19,752,593 out of 20,488,804
Mismatches: 469,841 out of 20,488,804
Insertions: 47,187 out of 20,488,804

Anopheles merus

Uncovered: 103,095,796 out of 288,048,996
Covered: 184,953,200 out of 288,048,996

Uncovered: 385,084 out of 19,203,252
Matches: 18,338,865 out of 19,203,252
Mismatches: 436,832 out of 19,203,252
Insertions: 42,471 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 melas 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}