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Medaka vs Cod LastZ alignments

Medaka (Oryzias latipes, MEDAKA1) and Cod (Gadus morhua, gadMor1) 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 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: 371,272

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

Uncovered: 781,494,921 out of 868,983,502
Covered: 87,488,581 out of 868,983,502

Uncovered: 4,283,237 out of 30,193,605
Matches: 19,481,211 out of 30,193,605
Mismatches: 6,191,313 out of 30,193,605
Insertions: 237,844 out of 30,193,605

Gadus morhua

Uncovered: 767,165,612 out of 832,114,588
Covered: 64,948,976 out of 832,114,588

Uncovered: 5,868,530 out of 29,438,356
Matches: 17,799,738 out of 29,438,356
Mismatches: 5,501,412 out of 29,438,356
Insertions: 268,676 out of 29,438,356