Anopheles gambiae vs Anopheles epiroticus LastZ Results

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Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles epiroticus (Anopheles epiroticus, AepiE1) 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: 142,670

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

Uncovered: 106,055,782 out of 281,378,673
Covered: 175,322,891 out of 281,378,673

Uncovered: 347,153 out of 22,369,942
Matches: 18,026,689 out of 22,369,942
Mismatches: 3,611,402 out of 22,369,942
Insertions: 384,698 out of 22,369,942

Anopheles epiroticus

Uncovered: 70,921,218 out of 223,486,714
Covered: 152,565,496 out of 223,486,714

Uncovered: 202,104 out of 20,285,978
Matches: 16,476,448 out of 20,285,978
Mismatches: 3,353,680 out of 20,285,978
Insertions: 253,746 out of 20,285,978

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 Anopheles epiroticus
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}