Drosophila melanogaster vs Drosophila virilis LastZ Results

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Drosophila melanogaster (Drosophila melanogaster, BDGP6) and Drosophila virilis (Drosophila virilis, dvir_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: 139,819

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

Uncovered: 85,351,473 out of 143,725,995
Covered: 58,374,522 out of 143,725,995

Uncovered: 2,228,824 out of 22,883,909
Matches: 14,937,664 out of 22,883,909
Mismatches: 5,155,438 out of 22,883,909
Insertions: 561,983 out of 22,883,909

Drosophila virilis

Uncovered: 146,111,855 out of 206,026,697
Covered: 59,914,842 out of 206,026,697

Uncovered: 1,894,977 out of 21,742,881
Matches: 14,291,551 out of 21,742,881
Mismatches: 4,900,459 out of 21,742,881
Insertions: 655,894 out of 21,742,881

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 virilis
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}