Anopheles albimanus vs Anopheles minimus LastZ Results

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Anopheles albimanus (Anopheles albimanus, AalbS2) and Anopheles minimus (Anopheles minimus, AminM1) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release . Anopheles albimanus 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: 107,938

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

Uncovered: 136,643,751 out of 173,339,240
Covered: 36,695,489 out of 173,339,240

Uncovered: 1,760,443 out of 20,837,397
Matches: 13,814,206 out of 20,837,397
Mismatches: 4,553,679 out of 20,837,397
Insertions: 709,069 out of 20,837,397

Anopheles minimus

Uncovered: 165,682,795 out of 201,793,324
Covered: 36,110,529 out of 201,793,324

Uncovered: 1,883,888 out of 20,952,760
Matches: 13,977,403 out of 20,952,760
Mismatches: 4,626,619 out of 20,952,760
Insertions: 464,850 out of 20,952,760

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 albimanus Anopheles minimus
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}