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 VectorBase release 1502. 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: 78,524

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

Uncovered: 62,690,712 out of 273,109,044
Covered: 210,418,332 out of 273,109,044

Uncovered: 1,446,815 out of 20,801,863
Matches: 19,110,144 out of 20,801,863
Mismatches: 218,518 out of 20,801,863
Insertions: 26,386 out of 20,801,863

Anopheles coluzzii

Uncovered: 26,501,418 out of 224,455,335
Covered: 197,953,917 out of 224,455,335

Uncovered: 482,367 out of 19,049,684
Matches: 18,355,431 out of 19,049,684
Mismatches: 193,899 out of 19,049,684
Insertions: 17,987 out of 19,049,684

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 --identity=80..100 --matchcount=1000

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}