Anopheles gambiae vs Anopheles maculatus LastZ Results

Back to all analyses

Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles maculatus (Anopheles maculatus, AmacM1) 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: 153,964

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

Uncovered: 179,220,590 out of 273,109,044
Covered: 93,888,454 out of 273,109,044

Uncovered: 3,699,761 out of 20,801,863
Matches: 13,600,391 out of 20,801,863
Mismatches: 3,176,037 out of 20,801,863
Insertions: 325,674 out of 20,801,863

Anopheles maculatus

Uncovered: 57,674,489 out of 141,894,015
Covered: 84,219,526 out of 141,894,015

Uncovered: 625,163 out of 16,389,058
Matches: 12,608,175 out of 16,389,058
Mismatches: 2,879,629 out of 16,389,058
Insertions: 276,091 out of 16,389,058

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 maculatus
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}