Drosophila melanogaster vs Drosophila grimshawi LastZ Results

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Drosophila melanogaster (Drosophila melanogaster, BDGP6) and Drosophila grimshawi (Drosophila grimshawi, dgri_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: 151,878

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

Uncovered: 87,712,045 out of 143,725,995
Covered: 56,013,950 out of 143,725,995

Uncovered: 2,482,806 out of 22,883,909
Matches: 14,704,150 out of 22,883,909
Mismatches: 5,154,999 out of 22,883,909
Insertions: 541,954 out of 22,883,909

Drosophila grimshawi

Uncovered: 138,085,817 out of 200,467,819
Covered: 62,382,002 out of 200,467,819

Uncovered: 1,817,037 out of 22,291,763
Matches: 14,632,304 out of 22,291,763
Mismatches: 5,093,614 out of 22,291,763
Insertions: 748,808 out of 22,291,763

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 grimshawi
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}