Anopheles albimanus vs Anopheles coluzzii LastZ Results

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Anopheles albimanus (Anopheles albimanus, AalbS2) and Anopheles coluzzii (Anopheles coluzzii, AcolM1) 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: 104,370

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

Uncovered: 139,786,573 out of 173,339,240
Covered: 33,552,667 out of 173,339,240

Uncovered: 2,691,474 out of 20,837,397
Matches: 13,354,734 out of 20,837,397
Mismatches: 4,168,213 out of 20,837,397
Insertions: 622,976 out of 20,837,397

Anopheles coluzzii

Uncovered: 190,594,516 out of 224,455,335
Covered: 33,860,819 out of 224,455,335

Uncovered: 2,302,229 out of 19,167,019
Matches: 12,540,502 out of 19,167,019
Mismatches: 3,871,493 out of 19,167,019
Insertions: 452,795 out of 19,167,019

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 coluzzii
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}