Drosophila melanogaster vs Drosophila erecta LastZ Results

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Drosophila melanogaster (Drosophila melanogaster, BDGP6) and Drosophila erecta (Drosophila erecta, dere_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: 68,760

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

Uncovered: 28,302,753 out of 143,725,995
Covered: 115,423,242 out of 143,725,995

Uncovered: 154,340 out of 22,883,909
Matches: 20,780,433 out of 22,883,909
Mismatches: 1,826,084 out of 22,883,909
Insertions: 123,052 out of 22,883,909

Drosophila erecta

Uncovered: 35,241,477 out of 152,712,140
Covered: 117,470,663 out of 152,712,140

Uncovered: 156,776 out of 21,883,890
Matches: 19,876,034 out of 21,883,890
Mismatches: 1,711,621 out of 21,883,890
Insertions: 139,459 out of 21,883,890

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 erecta
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}