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Pig vs LastZ alignments

Pig (Sus scrofa, Sscrofa10.2) and (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.

Full list of pairwise alignments

Configuration parameters

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
Additional parameters --ambiguous=iupac
Scoring matrix (Q) Default

Chunking parameters

Pig
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: 2703457

Genome coverage(bp) Coding exon coverage (bp)
Pig
1,645,352,463 out of 2,808,526,148 29,449,193 out of 29,803,039
1,386,079,210 out of 2,670,422,299 28,176,193 out of 32,345,388