Drosophila melanogaster vs Drosophila ananassae LastZ Results

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Drosophila melanogaster (Drosophila melanogaster, BDGP6) and Drosophila ananassae (Drosophila ananassae, dana_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: 108,898

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

Uncovered: 50,596,083 out of 143,725,995
Covered: 93,129,912 out of 143,725,995

Uncovered: 919,309 out of 22,883,909
Matches: 16,847,635 out of 22,883,909
Mismatches: 4,696,635 out of 22,883,909
Insertions: 420,330 out of 22,883,909

Drosophila ananassae

Uncovered: 137,379,533 out of 230,993,012
Covered: 93,613,479 out of 230,993,012

Uncovered: 1,060,121 out of 22,156,670
Matches: 16,164,413 out of 22,156,670
Mismatches: 4,473,220 out of 22,156,670
Insertions: 458,916 out of 22,156,670

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 ananassae
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}