Anopheles gambiae vs Anopheles christyi LastZ Results

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Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles christyi (Anopheles christyi, AchrA1) 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: 140,778

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

Uncovered: 112,821,530 out of 273,109,044
Covered: 160,287,514 out of 273,109,044

Uncovered: 530,129 out of 20,801,863
Matches: 17,208,887 out of 20,801,863
Mismatches: 2,780,886 out of 20,801,863
Insertions: 281,961 out of 20,801,863

Anopheles christyi

Uncovered: 27,624,922 out of 172,658,580
Covered: 145,033,658 out of 172,658,580

Uncovered: 119,333 out of 17,806,837
Matches: 15,119,376 out of 17,806,837
Mismatches: 2,394,315 out of 17,806,837
Insertions: 173,813 out of 17,806,837

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 christyi
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}