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Medaka vs Platyfish LastZ alignments

Medaka (Oryzias latipes, MEDAKA1) and Platyfish (Xiphophorus maculatus, Xipmac4.4.2) 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)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

Medaka Platyfish
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: 502,213

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

Uncovered: 682,628,569 out of 868,983,502
Covered: 186,354,933 out of 868,983,502

Uncovered: 1,632,962 out of 30,193,605
Matches: 22,728,386 out of 30,193,605
Mismatches: 5,590,664 out of 30,193,605
Insertions: 241,593 out of 30,193,605

Xiphophorus maculatus

Uncovered: 579,744,615 out of 729,662,853
Covered: 149,918,238 out of 729,662,853

Uncovered: 2,911,756 out of 33,480,785
Matches: 24,266,599 out of 33,480,785
Mismatches: 5,980,466 out of 33,480,785
Insertions: 321,964 out of 33,480,785