Drosophila melanogaster vs Belgica antarctica LastZ Results

Back to all analyses

Drosophila melanogaster (Drosophila melanogaster, BDGP6) and Belgica antarctica (Belgica antarctica, ASM77530v1) 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: 35,453

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

Uncovered: 132,821,817 out of 143,725,995
Covered: 10,904,178 out of 143,725,995

Uncovered: 13,004,784 out of 22,848,419
Matches: 6,249,746 out of 22,848,419
Mismatches: 3,257,501 out of 22,848,419
Insertions: 336,388 out of 22,848,419

Belgica antarctica

Uncovered: 78,764,060 out of 89,583,723
Covered: 10,819,663 out of 89,583,723

Uncovered: 9,823,678 out of 18,676,815
Matches: 5,665,144 out of 18,676,815
Mismatches: 2,959,539 out of 18,676,815
Insertions: 228,454 out of 18,676,815

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 Belgica antarctica
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}