Aedes aegypti vs Culex quinquefasciatus LastZ Results

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Aedes aegypti (Aedes aegypti, AaegL3) and Culex quinquefasciatus (Culex quinquefasciatus, CpipJ2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release . Aedes aegypti 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: 140,085

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

Uncovered: 1,336,530,187 out of 1,383,974,186
Covered: 47,443,999 out of 1,383,974,186

Uncovered: 2,755,473 out of 22,630,251
Matches: 14,402,460 out of 22,630,251
Mismatches: 5,022,619 out of 22,630,251
Insertions: 449,699 out of 22,630,251

Culex quinquefasciatus

Uncovered: 534,221,688 out of 579,057,705
Covered: 44,836,017 out of 579,057,705

Uncovered: 4,137,216 out of 24,941,119
Matches: 15,018,538 out of 24,941,119
Mismatches: 5,306,516 out of 24,941,119
Insertions: 478,849 out of 24,941,119

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 Culex quinquefasciatus
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}