Drosophila melanogaster vs Drosophila yakuba LastZ Results

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Drosophila melanogaster (Drosophila melanogaster, BDGP6) and Drosophila yakuba (Drosophila yakuba, dyak_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: 75,139

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

Uncovered: 29,098,696 out of 143,725,995
Covered: 114,627,299 out of 143,725,995

Uncovered: 268,181 out of 22,883,909
Matches: 20,654,570 out of 22,883,909
Mismatches: 1,851,910 out of 22,883,909
Insertions: 109,248 out of 22,883,909

Drosophila yakuba

Uncovered: 41,795,860 out of 165,693,946
Covered: 123,898,086 out of 165,693,946

Uncovered: 392,730 out of 22,634,633
Matches: 20,277,222 out of 22,634,633
Mismatches: 1,798,814 out of 22,634,633
Insertions: 165,867 out of 22,634,633

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 yakuba
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}