Anopheles gambiae vs Anopheles melas LastZ Results

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Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles melas (Anopheles melas, AmelC2) 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: 94,617

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

Uncovered: 77,592,098 out of 273,109,044
Covered: 195,516,946 out of 273,109,044

Uncovered: 798,944 out of 20,801,863
Matches: 19,550,778 out of 20,801,863
Mismatches: 416,199 out of 20,801,863
Insertions: 35,942 out of 20,801,863

Anopheles melas

Uncovered: 33,267,868 out of 224,162,116
Covered: 190,894,248 out of 224,162,116

Uncovered: 266,291 out of 20,488,804
Matches: 19,757,316 out of 20,488,804
Mismatches: 419,914 out of 20,488,804
Insertions: 45,283 out of 20,488,804

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 --identity=80..100 --matchcount=1000

Chunking parameters

Anopheles gambiae Anopheles melas
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}