Drosophila melanogaster vs Drosophila willistoni LastZ Results

Back to all analyses

Drosophila melanogaster (Drosophila melanogaster, BDGP6) and Drosophila willistoni (Drosophila willistoni, dwil_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: 150,879

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

Uncovered: 84,197,643 out of 143,725,995
Covered: 59,528,352 out of 143,725,995

Uncovered: 2,059,284 out of 22,883,909
Matches: 14,854,486 out of 22,883,909
Mismatches: 5,417,654 out of 22,883,909
Insertions: 552,485 out of 22,883,909

Drosophila willistoni

Uncovered: 171,407,449 out of 235,516,348
Covered: 64,108,899 out of 235,516,348

Uncovered: 2,398,430 out of 22,675,476
Matches: 14,335,163 out of 22,675,476
Mismatches: 5,212,547 out of 22,675,476
Insertions: 729,336 out of 22,675,476

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 willistoni
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}