Anopheles coluzzii vs Anopheles melas LastZ Results

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Anopheles coluzzii (Anopheles coluzzii, AcolM1) and Anopheles melas (Anopheles melas, AmelC2) 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: 81,332

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

Uncovered: 47,892,830 out of 224,455,335
Covered: 176,562,505 out of 224,455,335

Uncovered: 880,196 out of 19,049,684
Matches: 17,748,422 out of 19,049,684
Mismatches: 382,957 out of 19,049,684
Insertions: 38,109 out of 19,049,684

Anopheles melas

Uncovered: 42,239,816 out of 224,162,116
Covered: 181,922,300 out of 224,162,116

Uncovered: 1,503,700 out of 20,488,804
Matches: 18,531,686 out of 20,488,804
Mismatches: 402,995 out of 20,488,804
Insertions: 50,423 out of 20,488,804

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 melas
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}