Anopheles gambiae vs Aedes aegypti LastZ Results

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Anopheles gambiae (Anopheles gambiae, AgamP4) and Aedes aegypti (Aedes aegypti, AaegL3) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release . Anopheles gambiae 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: 66,525

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

Uncovered: 250,585,369 out of 273,109,044
Covered: 22,523,675 out of 273,109,044

Uncovered: 4,594,970 out of 21,237,323
Matches: 11,315,783 out of 21,237,323
Mismatches: 4,654,765 out of 21,237,323
Insertions: 671,805 out of 21,237,323

Aedes aegypti

Uncovered: 1,358,918,840 out of 1,383,974,186
Covered: 25,055,346 out of 1,383,974,186

Uncovered: 5,539,481 out of 22,630,251
Matches: 11,849,080 out of 22,630,251
Mismatches: 4,933,632 out of 22,630,251
Insertions: 308,058 out of 22,630,251

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 gambiae Aedes aegypti
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}