Anopheles albimanus vs Anopheles stephensi LastZ Results

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Anopheles albimanus (Anopheles albimanus, AalbS2) and Anopheles stephensi (Anopheles stephensi, AsteS1) 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: 106,039

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

Uncovered: 137,486,742 out of 173,339,240
Covered: 35,852,498 out of 173,339,240

Uncovered: 1,702,255 out of 20,837,397
Matches: 13,993,165 out of 20,837,397
Mismatches: 4,450,833 out of 20,837,397
Insertions: 691,144 out of 20,837,397

Anopheles stephensi

Uncovered: 189,605,505 out of 225,369,006
Covered: 35,763,501 out of 225,369,006

Uncovered: 1,886,482 out of 21,152,822
Matches: 14,210,723 out of 21,152,822
Mismatches: 4,537,358 out of 21,152,822
Insertions: 518,259 out of 21,152,822

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 stephensi
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}