Anopheles gambiae vs Culex quinquefasciatus LastZ Results

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Anopheles gambiae (Anopheles gambiae, AgamP4) and Culex quinquefasciatus (Culex quinquefasciatus, CpipJ2) 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: 65,311

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

Uncovered: 250,693,942 out of 273,109,044
Covered: 22,415,102 out of 273,109,044

Uncovered: 4,398,285 out of 21,237,323
Matches: 11,574,255 out of 21,237,323
Mismatches: 4,502,703 out of 21,237,323
Insertions: 762,080 out of 21,237,323

Culex quinquefasciatus

Uncovered: 554,505,769 out of 579,057,705
Covered: 24,551,936 out of 579,057,705

Uncovered: 7,128,277 out of 24,941,119
Matches: 12,499,040 out of 24,941,119
Mismatches: 4,920,844 out of 24,941,119
Insertions: 392,958 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

Anopheles gambiae 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}