Anopheles gambiae vs Anopheles atroparvus LastZ Results

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Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles atroparvus (Anopheles atroparvus, AatrE3) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa 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: 172,975

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

Uncovered: 207,637,718 out of 281,378,673
Covered: 73,740,955 out of 281,378,673

Uncovered: 1,373,609 out of 22,369,942
Matches: 15,595,265 out of 22,369,942
Mismatches: 4,877,464 out of 22,369,942
Insertions: 523,604 out of 22,369,942

Anopheles atroparvus

Uncovered: 159,275,666 out of 225,295,225
Covered: 66,019,559 out of 225,295,225

Uncovered: 1,310,580 out of 20,693,284
Matches: 14,495,182 out of 20,693,284
Mismatches: 4,344,067 out of 20,693,284
Insertions: 543,455 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}