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Zebrafish vs Cod LastZ alignments

Zebrafish (Danio rerio, Zv9) and Cod (Gadus morhua, gadMor1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 65. 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)50
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 Cod
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}

Results

Number of alignment blocks: 297,047

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

Uncovered: 1,350,925,463 out of 1,412,464,843
Covered: 61,539,380 out of 1,412,464,843

Uncovered: 12,159,678 out of 42,417,757
Matches: 21,650,675 out of 42,417,757
Mismatches: 8,233,750 out of 42,417,757
Insertions: 373,654 out of 42,417,757

Gadus morhua

Uncovered: 789,803,438 out of 832,114,588
Covered: 42,311,150 out of 832,114,588

Uncovered: 8,245,915 out of 29,438,356
Matches: 15,363,354 out of 29,438,356
Mismatches: 5,528,232 out of 29,438,356
Insertions: 300,855 out of 29,438,356