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 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: 144,552

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

Uncovered: 50,065,266 out of 281,378,673
Covered: 231,313,407 out of 281,378,673

Uncovered: 354,119 out of 22,369,942
Matches: 20,959,114 out of 22,369,942
Mismatches: 1,009,582 out of 22,369,942
Insertions: 47,127 out of 22,369,942

Anopheles melas

Uncovered: 15,394,707 out of 224,162,116
Covered: 208,767,409 out of 224,162,116

Uncovered: 134,997 out of 20,575,065
Matches: 19,608,999 out of 20,575,065
Mismatches: 786,122 out of 20,575,065
Insertions: 44,947 out of 20,575,065

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 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}