Aedes aegypti (LVP_AGWG) vs Aedes albopictus LastZ Results

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Aedes aegypti (LVP_AGWG) (Aedes aegypti, AaegL5) and Aedes albopictus (Aedes albopictus, AaloF1) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release . Aedes aegypti (LVP_AGWG) 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: 552,090

Genome coverage (bp) Coding exon coverage (bp)
Aedes aegypti

Uncovered: 1,115,113,608 out of 1,278,732,104
Covered: 163,618,496 out of 1,278,732,104

Uncovered: 1,094,303 out of 24,249,714
Matches: 19,336,838 out of 24,249,714
Mismatches: 3,645,627 out of 24,249,714
Insertions: 172,946 out of 24,249,714

Aedes albopictus

Uncovered: 1,680,878,412 out of 1,923,476,627
Covered: 242,598,215 out of 1,923,476,627

Uncovered: 1,843,099 out of 24,217,773
Matches: 18,625,218 out of 24,217,773
Mismatches: 3,489,870 out of 24,217,773
Insertions: 259,586 out of 24,217,773

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

Aedes aegypti (LVP_AGWG) Aedes albopictus
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}