Aedes albopictus vs Aedes aegypti (LVP_AGWG) LastZ Results

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Aedes albopictus (Aedes albopictus, AaloF1) and Aedes aegypti (LVP_AGWG) (Aedes aegypti, AaegL5) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release . Aedes albopictus 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: 552,279

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

Uncovered: 1,680,971,019 out of 1,923,476,627
Covered: 242,505,608 out of 1,923,476,627

Uncovered: 1,845,058 out of 24,217,773
Matches: 18,624,323 out of 24,217,773
Mismatches: 3,489,751 out of 24,217,773
Insertions: 258,641 out of 24,217,773

Aedes aegypti

Uncovered: 1,115,052,069 out of 1,278,732,104
Covered: 163,680,035 out of 1,278,732,104

Uncovered: 1,093,788 out of 24,304,798
Matches: 19,377,947 out of 24,304,798
Mismatches: 3,658,808 out of 24,304,798
Insertions: 174,255 out of 24,304,798

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 albopictus Aedes aegypti (LVP_AGWG)
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}