Anopheles gambiae vs Anopheles atroparvus LastZ Results

Back to all analyses

Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles atroparvus (Anopheles atroparvus, AatrE3) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release . Anopheles gambiae 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: 172,829

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

Uncovered: 199,935,369 out of 273,109,044
Covered: 73,173,675 out of 273,109,044

Uncovered: 1,205,972 out of 21,473,329
Matches: 15,074,147 out of 21,473,329
Mismatches: 4,706,949 out of 21,473,329
Insertions: 486,261 out of 21,473,329

Anopheles atroparvus

Uncovered: 158,710,926 out of 225,295,225
Covered: 66,584,299 out of 225,295,225

Uncovered: 1,279,260 out of 20,693,284
Matches: 14,579,506 out of 20,693,284
Mismatches: 4,287,642 out of 20,693,284
Insertions: 546,876 out of 20,693,284

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 gambiae Anopheles atroparvus
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}