Anopheles gambiae vs Anopheles dirus LastZ Results

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Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles dirus (Anopheles dirus, AdirW1) 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: 200,021

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

Uncovered: 161,359,360 out of 281,378,673
Covered: 120,019,313 out of 281,378,673

Uncovered: 703,890 out of 22,369,942
Matches: 16,875,145 out of 22,369,942
Mismatches: 4,264,630 out of 22,369,942
Insertions: 526,277 out of 22,369,942

Anopheles dirus

Uncovered: 112,112,188 out of 216,307,690
Covered: 104,195,502 out of 216,307,690

Uncovered: 581,333 out of 21,096,405
Matches: 15,925,254 out of 21,096,405
Mismatches: 4,184,656 out of 21,096,405
Insertions: 405,162 out of 21,096,405

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 dirus
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}