Anopheles stephensi vs Anopheles stephensi (Indian) LastZ Results

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Anopheles stephensi (Anopheles stephensi, AsteS1) and Anopheles stephensi (Indian) (Anopheles stephensi, AsteI2) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release 1502. Anopheles stephensi 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: 36,292

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

Uncovered: 35,588,390 out of 225,369,006
Covered: 189,780,616 out of 225,369,006

Uncovered: 127,560 out of 21,130,775
Matches: 20,886,026 out of 21,130,775
Mismatches: 105,843 out of 21,130,775
Insertions: 11,346 out of 21,130,775

Anopheles stephensi

Uncovered: 31,529,333 out of 221,324,304
Covered: 189,794,971 out of 221,324,304

Uncovered: 202,904 out of 20,271,658
Matches: 19,963,513 out of 20,271,658
Mismatches: 98,409 out of 20,271,658
Insertions: 6,832 out of 20,271,658

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 stephensi Anopheles stephensi (Indian)
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}