Anopheles gambiae vs Anopheles coluzzii LastZ Results

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Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles coluzzii (Anopheles coluzzii, AcolM1) 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: 111,081

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

Uncovered: 37,933,321 out of 281,378,673
Covered: 243,445,352 out of 281,378,673

Uncovered: 502,369 out of 22,369,942
Matches: 20,219,767 out of 22,369,942
Mismatches: 1,617,247 out of 22,369,942
Insertions: 30,559 out of 22,369,942

Anopheles coluzzii

Uncovered: 9,126,987 out of 224,455,335
Covered: 215,328,348 out of 224,455,335

Uncovered: 343,849 out of 19,279,148
Matches: 18,297,163 out of 19,279,148
Mismatches: 617,963 out of 19,279,148
Insertions: 20,173 out of 19,279,148

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 coluzzii
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}