Anopheles albimanus vs Anopheles funestus LastZ Results

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Anopheles albimanus (Anopheles albimanus, AalbS2) and Anopheles funestus (Anopheles funestus, AfunF3) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release . Anopheles albimanus 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: 108,732

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

Uncovered: 137,967,324 out of 173,339,240
Covered: 35,371,916 out of 173,339,240

Uncovered: 2,288,015 out of 20,938,803
Matches: 13,449,108 out of 20,938,803
Mismatches: 4,515,263 out of 20,938,803
Insertions: 686,417 out of 20,938,803

Anopheles funestus

Uncovered: 170,474,454 out of 210,989,154
Covered: 40,514,700 out of 210,989,154

Uncovered: 2,039,200 out of 22,083,846
Matches: 14,513,306 out of 22,083,846
Mismatches: 5,043,266 out of 22,083,846
Insertions: 488,074 out of 22,083,846

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 albimanus Anopheles funestus
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}