Anopheles gambiae vs Anopheles albimanus LastZ Results

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Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles albimanus (Anopheles albimanus, AalbS2) 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: 114,074

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

Uncovered: 241,097,931 out of 281,378,673
Covered: 40,280,742 out of 281,378,673

Uncovered: 2,105,026 out of 22,369,942
Matches: 14,854,514 out of 22,369,942
Mismatches: 4,845,704 out of 22,369,942
Insertions: 564,698 out of 22,369,942

Anopheles albimanus

Uncovered: 136,521,984 out of 173,339,240
Covered: 36,817,256 out of 173,339,240

Uncovered: 1,630,813 out of 20,938,803
Matches: 13,904,844 out of 20,938,803
Mismatches: 4,731,264 out of 20,938,803
Insertions: 671,882 out of 20,938,803

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 albimanus
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}