Drosophila melanogaster vs Drosophila pseudoobscura LastZ Results

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Drosophila melanogaster (Drosophila melanogaster, BDGP6) and Drosophila pseudoobscura (Drosophila pseudoobscura pseudoobscura, Dpse_3.0) 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: 144,039

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

Uncovered: 62,262,124 out of 143,725,995
Covered: 81,463,871 out of 143,725,995

Uncovered: 1,467,124 out of 22,883,909
Matches: 16,158,850 out of 22,883,909
Mismatches: 4,808,970 out of 22,883,909
Insertions: 448,965 out of 22,883,909

Drosophila pseudoobscura pseudoobscura

Uncovered: 64,901,657 out of 152,696,192
Covered: 87,794,535 out of 152,696,192

Uncovered: 1,870,735 out of 23,277,461
Matches: 15,976,116 out of 23,277,461
Mismatches: 4,770,451 out of 23,277,461
Insertions: 660,159 out of 23,277,461

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 pseudoobscura
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}