Drosophila melanogaster vs Mayetiola destructor LastZ Results

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Drosophila melanogaster (Drosophila melanogaster, BDGP6) and Mayetiola destructor (Mayetiola destructor, Mdes_1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release . Drosophila melanogaster 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: 36,364

Genome coverage (bp) Coding exon coverage (bp)
Drosophila melanogaster

Uncovered: 132,457,566 out of 143,725,995
Covered: 11,268,429 out of 143,725,995

Uncovered: 13,640,395 out of 22,848,419
Matches: 5,716,417 out of 22,848,419
Mismatches: 3,275,547 out of 22,848,419
Insertions: 216,060 out of 22,848,419

Mayetiola destructor

Uncovered: 174,788,331 out of 185,827,756
Covered: 11,039,425 out of 185,827,756

Uncovered: 14,014,671 out of 22,605,432
Matches: 5,446,876 out of 22,605,432
Mismatches: 2,945,339 out of 22,605,432
Insertions: 198,546 out of 22,605,432

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

Drosophila melanogaster Mayetiola destructor
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}