Anopheles gambiae vs Anopheles stephensi LastZ Results

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Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles stephensi (Anopheles stephensi, AsteS1) 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: 187,275

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

Uncovered: 134,375,243 out of 281,378,673
Covered: 147,003,430 out of 281,378,673

Uncovered: 544,448 out of 22,369,942
Matches: 17,180,723 out of 22,369,942
Mismatches: 4,202,359 out of 22,369,942
Insertions: 442,412 out of 22,369,942

Anopheles stephensi

Uncovered: 94,899,668 out of 225,369,006
Covered: 130,469,338 out of 225,369,006

Uncovered: 396,509 out of 21,181,416
Matches: 16,382,792 out of 21,181,416
Mismatches: 4,028,833 out of 21,181,416
Insertions: 373,282 out of 21,181,416

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 stephensi
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}