Anopheles sinensis vs Anopheles sinensis (China) LastZ Results

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Anopheles sinensis (Anopheles sinensis, AsinS2) and Anopheles sinensis (China) (Anopheles sinensis, AsinC2) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release 1508. Anopheles sinensis 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: 80,512

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

Uncovered: 197,744,763 out of 375,763,635
Covered: 178,018,872 out of 375,763,635

Uncovered: 276,948 out of 17,240,992
Matches: 16,706,102 out of 17,240,992
Mismatches: 241,464 out of 17,240,992
Insertions: 16,478 out of 17,240,992

Anopheles sinensis

Uncovered: 40,709,839 out of 220,777,669
Covered: 180,067,830 out of 220,777,669

Uncovered: 1,519,715 out of 21,901,593
Matches: 20,054,874 out of 21,901,593
Mismatches: 302,745 out of 21,901,593
Insertions: 24,259 out of 21,901,593

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=90..100 --matchcount=1000

Chunking parameters

Anopheles sinensis Anopheles sinensis (China)
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}