Drosophila melanogaster vs Megaselia scalaris LastZ Results

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Drosophila melanogaster (Drosophila melanogaster, BDGP6) and Megaselia scalaris (Megaselia scalaris, Msca1) 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: 30,956

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

Uncovered: 135,682,437 out of 143,725,995
Covered: 8,043,558 out of 143,725,995

Uncovered: 15,781,990 out of 22,883,909
Matches: 4,546,093 out of 22,883,909
Mismatches: 2,356,737 out of 22,883,909
Insertions: 199,089 out of 22,883,909

Megaselia scalaris

Uncovered: 482,231,722 out of 490,071,573
Covered: 7,839,851 out of 490,071,573

Uncovered: 3,532,449 out of 7,743,281
Matches: 2,726,630 out of 7,743,281
Mismatches: 1,413,629 out of 7,743,281
Insertions: 70,573 out of 7,743,281

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 Megaselia scalaris
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}