Anopheles gambiae vs Anopheles atroparvus LastZ Results

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Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles atroparvus (Anopheles atroparvus, AatrE2) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase 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: 167,250

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

Uncovered: 202,601,805 out of 273,109,044
Covered: 70,507,239 out of 273,109,044

Uncovered: 1,237,953 out of 21,473,329
Matches: 15,087,444 out of 21,473,329
Mismatches: 4,661,592 out of 21,473,329
Insertions: 486,340 out of 21,473,329

Anopheles atroparvus

Uncovered: 159,638,095 out of 224,290,125
Covered: 64,652,030 out of 224,290,125

Uncovered: 1,338,554 out of 20,701,390
Matches: 14,549,064 out of 20,701,390
Mismatches: 4,266,944 out of 20,701,390
Insertions: 546,828 out of 20,701,390

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 atroparvus
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}