Anopheles albimanus vs Anopheles maculatus LastZ Results

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Anopheles albimanus (Anopheles albimanus, AalbS2) and Anopheles maculatus (Anopheles maculatus, AmacM1) 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: 73,498

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

Uncovered: 146,782,209 out of 173,339,240
Covered: 26,557,031 out of 173,339,240

Uncovered: 5,002,504 out of 20,837,397
Matches: 11,512,281 out of 20,837,397
Mismatches: 3,786,791 out of 20,837,397
Insertions: 535,821 out of 20,837,397

Anopheles maculatus

Uncovered: 116,427,183 out of 141,894,015
Covered: 25,466,832 out of 141,894,015

Uncovered: 1,855,408 out of 16,388,318
Matches: 10,690,455 out of 16,388,318
Mismatches: 3,475,666 out of 16,388,318
Insertions: 366,789 out of 16,388,318

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 maculatus
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}