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Pig vs Cow LastZ alignments

Pig (Sus scrofa, Sscrofa10.2) and Cow (Bos taurus, UMD3.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 67. Pig 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)
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

Pig Cow
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: 2,703,457

Genome coverage (bp) Coding exon coverage (bp)
Sus scrofa

Uncovered: 1,163,173,685 out of 2,808,526,148
Covered: 1,645,352,463 out of 2,808,526,148

Uncovered: 354,381 out of 29,865,122
Matches: 26,415,918 out of 29,865,122
Mismatches: 2,960,891 out of 29,865,122
Insertions: 133,932 out of 29,865,122

Bos taurus

Uncovered: 1,284,343,089 out of 2,670,422,299
Covered: 1,386,079,210 out of 2,670,422,299

Uncovered: 4,169,445 out of 32,345,388
Matches: 25,274,819 out of 32,345,388
Mismatches: 2,789,420 out of 32,345,388
Insertions: 111,704 out of 32,345,388