Anopheles albimanus vs Anopheles melas LastZ Results

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Anopheles albimanus (Anopheles albimanus, AalbS2) and Anopheles melas (Anopheles melas, AmelC2) 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: 102,932

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

Uncovered: 139,519,998 out of 173,339,240
Covered: 33,819,242 out of 173,339,240

Uncovered: 1,909,578 out of 20,837,397
Matches: 13,929,392 out of 20,837,397
Mismatches: 4,338,053 out of 20,837,397
Insertions: 660,374 out of 20,837,397

Anopheles melas

Uncovered: 188,900,669 out of 224,162,116
Covered: 35,261,447 out of 224,162,116

Uncovered: 1,871,757 out of 20,521,237
Matches: 13,881,904 out of 20,521,237
Mismatches: 4,237,060 out of 20,521,237
Insertions: 530,516 out of 20,521,237

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 melas
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}