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 VectorBase release 1506. 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: 163,657

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

Uncovered: 107,379,828 out of 273,109,044
Covered: 165,729,216 out of 273,109,044

Uncovered: 304,056 out of 20,801,863
Matches: 17,076,890 out of 20,801,863
Mismatches: 3,070,697 out of 20,801,863
Insertions: 350,220 out of 20,801,863

Anopheles epiroticus

Uncovered: 72,781,258 out of 223,486,714
Covered: 150,705,456 out of 223,486,714

Uncovered: 199,443 out of 20,217,845
Matches: 16,770,172 out of 20,217,845
Mismatches: 2,987,757 out of 20,217,845
Insertions: 260,473 out of 20,217,845

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}