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Stickleback vs Cod LastZ alignments

Stickleback (Gasterosteus aculeatus, BROADS1) and Cod (Gadus morhua, gadMor1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 64. Stickleback 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)5000
Threshold for alignments between gapped alignment blocks (H)3000
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

Stickleback Cod
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: 300,871

Genome coverage (bp) Coding exon coverage (bp)
Gasterosteus aculeatus

Uncovered: 380,430,380 out of 461,533,448
Covered: 81,103,068 out of 461,533,448

Uncovered: 4,267,492 out of 32,649,418
Matches: 21,937,918 out of 32,649,418
Mismatches: 6,165,769 out of 32,649,418
Insertions: 278,239 out of 32,649,418

Gadus morhua

Uncovered: 757,262,201 out of 832,114,588
Covered: 74,852,387 out of 832,114,588

Uncovered: 4,438,538 out of 29,438,356
Matches: 19,494,973 out of 29,438,356
Mismatches: 5,330,472 out of 29,438,356
Insertions: 174,373 out of 29,438,356