Anopheles coluzzii vs Anopheles merus LastZ Results

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Anopheles coluzzii (Anopheles coluzzii, AcolM1) and Anopheles merus (Anopheles merus, AmerM2) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release 1506. Anopheles coluzzii 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: 79,771

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

Uncovered: 39,624,621 out of 224,455,335
Covered: 184,830,714 out of 224,455,335

Uncovered: 534,718 out of 19,049,684
Matches: 18,075,559 out of 19,049,684
Mismatches: 400,580 out of 19,049,684
Insertions: 38,827 out of 19,049,684

Anopheles merus

Uncovered: 102,598,000 out of 288,048,996
Covered: 185,450,996 out of 288,048,996

Uncovered: 1,241,078 out of 19,203,252
Matches: 17,525,559 out of 19,203,252
Mismatches: 390,584 out of 19,203,252
Insertions: 46,031 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 coluzzii 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}