Aedes aegypti (LVP_AGWG) vs Anopheles gambiae LastZ Results

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Aedes aegypti (LVP_AGWG) (Aedes aegypti, AaegL5) and Anopheles gambiae (Anopheles gambiae, AgamP4) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release . Aedes aegypti (LVP_AGWG) 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: 62,044

Genome coverage (bp) Coding exon coverage (bp)
Aedes aegypti

Uncovered: 1,255,804,357 out of 1,278,732,104
Covered: 22,927,747 out of 1,278,732,104

Uncovered: 6,552,476 out of 24,249,714
Matches: 12,274,204 out of 24,249,714
Mismatches: 5,079,423 out of 24,249,714
Insertions: 343,611 out of 24,249,714

Anopheles gambiae

Uncovered: 251,088,590 out of 273,109,044
Covered: 22,020,454 out of 273,109,044

Uncovered: 4,706,730 out of 21,473,329
Matches: 11,499,361 out of 21,473,329
Mismatches: 4,583,401 out of 21,473,329
Insertions: 683,837 out of 21,473,329

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

Aedes aegypti (LVP_AGWG) Anopheles gambiae
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}