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Medaka vs Tilapia LastZ alignments

Medaka (Oryzias latipes, MEDAKA1) and Tilapia (Oreochromis niloticus, Orenil1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 71. Medaka 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)5000
Threshold for gapped extension (L)5000
Threshold for alignments between gapped alignment blocks (H)3000
Masking count (M)2
Seed and Transition value (T)2
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

Medaka Tilapia
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: 472,601

Genome coverage (bp) Coding exon coverage (bp)
Oryzias latipes

Uncovered: 670,112,867 out of 868,983,502
Covered: 198,870,635 out of 868,983,502

Uncovered: 1,484,304 out of 30,193,605
Matches: 23,148,324 out of 30,193,605
Mismatches: 5,395,534 out of 30,193,605
Insertions: 165,443 out of 30,193,605

Oreochromis niloticus

Uncovered: 756,615,546 out of 927,383,394
Covered: 170,767,848 out of 927,383,394

Uncovered: 5,910,149 out of 37,304,121
Matches: 25,123,034 out of 37,304,121
Mismatches: 5,881,009 out of 37,304,121
Insertions: 389,929 out of 37,304,121