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Zebrafish vs Spotted gar LastZ alignments

Zebrafish (Danio rerio, Zv9) and Spotted gar (Lepisosteus oculatus, LepOcu1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 74. Zebrafish 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.

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)3000
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

Chunking parameters

Zebrafish Spotted gar
Chunk size 30,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}

Results

Number of alignment blocks: 279,676

Genome coverage (bp) Coding exon coverage (bp)
Danio rerio

Uncovered: 1,350,843,603 out of 1,412,464,843
Covered: 61,621,240 out of 1,412,464,843

Uncovered: 9,915,514 out of 42,682,327
Matches: 23,237,531 out of 42,682,327
Mismatches: 9,080,845 out of 42,682,327
Insertions: 448,437 out of 42,682,327

Lepisosteus oculatus

Uncovered: 902,230,246 out of 945,878,036
Covered: 43,647,790 out of 945,878,036

Uncovered: 7,762,099 out of 31,448,193
Matches: 16,889,168 out of 31,448,193
Mismatches: 6,391,155 out of 31,448,193
Insertions: 405,771 out of 31,448,193