Anopheles gambiae vs Anopheles culicifacies LastZ Results

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Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles culicifacies (Anopheles culicifacies, AculA1) 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: 182,241

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

Uncovered: 137,864,998 out of 281,378,673
Covered: 143,513,675 out of 281,378,673

Uncovered: 697,876 out of 22,369,942
Matches: 16,972,193 out of 22,369,942
Mismatches: 4,241,056 out of 22,369,942
Insertions: 458,817 out of 22,369,942

Anopheles culicifacies

Uncovered: 76,976,232 out of 202,998,806
Covered: 126,022,574 out of 202,998,806

Uncovered: 381,251 out of 20,923,336
Matches: 16,039,039 out of 20,923,336
Mismatches: 4,192,734 out of 20,923,336
Insertions: 310,312 out of 20,923,336

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 culicifacies
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}