Anopheles gambiae vs Anopheles culicifacies LastZ Results

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Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles culicifacies (Anopheles culicifacies, AculA1) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release 1506. 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: 196,747

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

Uncovered: 136,629,087 out of 273,109,044
Covered: 136,479,957 out of 273,109,044

Uncovered: 578,048 out of 20,801,863
Matches: 16,034,443 out of 20,801,863
Mismatches: 3,776,778 out of 20,801,863
Insertions: 412,594 out of 20,801,863

Anopheles culicifacies

Uncovered: 77,985,764 out of 202,998,806
Covered: 125,013,042 out of 202,998,806

Uncovered: 437,977 out of 20,895,716
Matches: 16,289,671 out of 20,895,716
Mismatches: 3,852,944 out of 20,895,716
Insertions: 315,124 out of 20,895,716

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 culicifacies
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}