Drosophila melanogaster vs Drosophila mojavensis LastZ Results

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Drosophila melanogaster (Drosophila melanogaster, BDGP6) and Drosophila mojavensis (Drosophila mojavensis, dmoj_caf1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release 78. 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: 138,831

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

Uncovered: 89,657,048 out of 143,725,995
Covered: 54,068,947 out of 143,725,995

Uncovered: 2,473,501 out of 22,883,909
Matches: 14,710,403 out of 22,883,909
Mismatches: 5,143,283 out of 22,883,909
Insertions: 556,722 out of 22,883,909

Drosophila mojavensis

Uncovered: 138,145,905 out of 193,826,310
Covered: 55,680,405 out of 193,826,310

Uncovered: 2,146,790 out of 21,624,806
Matches: 13,966,594 out of 21,624,806
Mismatches: 4,847,657 out of 21,624,806
Insertions: 663,765 out of 21,624,806

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 Drosophila mojavensis
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}