Anopheles gambiae vs Anopheles minimus LastZ Results

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Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles minimus (Anopheles minimus, AminM1) 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: 176,309

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

Uncovered: 126,829,022 out of 281,378,673
Covered: 154,549,651 out of 281,378,673

Uncovered: 545,647 out of 22,369,942
Matches: 17,061,380 out of 22,369,942
Mismatches: 4,299,386 out of 22,369,942
Insertions: 463,529 out of 22,369,942

Anopheles minimus

Uncovered: 69,831,924 out of 201,793,324
Covered: 131,961,400 out of 201,793,324

Uncovered: 357,905 out of 21,001,575
Matches: 16,163,552 out of 21,001,575
Mismatches: 4,196,425 out of 21,001,575
Insertions: 283,693 out of 21,001,575

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 minimus
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}