Anopheles gambiae vs Anopheles darlingi LastZ Results

Back to all analyses

Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles darlingi (Anopheles darlingi, AdarC3) 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: 93,291

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

Uncovered: 238,226,307 out of 273,109,044
Covered: 34,882,737 out of 273,109,044

Uncovered: 2,108,398 out of 21,237,323
Matches: 14,156,340 out of 21,237,323
Mismatches: 4,467,110 out of 21,237,323
Insertions: 505,475 out of 21,237,323

Anopheles darlingi

Uncovered: 103,605,898 out of 136,950,925
Covered: 33,345,027 out of 136,950,925

Uncovered: 1,419,080 out of 18,211,055
Matches: 12,265,900 out of 18,211,055
Mismatches: 3,987,223 out of 18,211,055
Insertions: 538,852 out of 18,211,055

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 darlingi
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}