Anopheles gambiae vs Anopheles funestus LastZ Results

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Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles funestus (Anopheles funestus, AfunF3) 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: 181,005

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

Uncovered: 136,786,666 out of 281,378,673
Covered: 144,592,007 out of 281,378,673

Uncovered: 1,124,843 out of 22,369,942
Matches: 16,769,606 out of 22,369,942
Mismatches: 4,038,000 out of 22,369,942
Insertions: 437,493 out of 22,369,942

Anopheles funestus

Uncovered: 76,528,212 out of 210,989,154
Covered: 134,460,942 out of 210,989,154

Uncovered: 452,169 out of 22,083,846
Matches: 16,877,745 out of 22,083,846
Mismatches: 4,459,111 out of 22,083,846
Insertions: 294,821 out of 22,083,846

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 funestus
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}