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Human vs Pig LastZ alignments

Human (Homo sapiens, GRCh37) and Pig (Sus scrofa, Sscrofa10.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 67. Human 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)
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

Human Pig
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}

Results

Number of alignment blocks: 2,109,059

Genome coverage (bp) Coding exon coverage (bp)
Homo sapiens

Uncovered: 1,734,396,939 out of 3,098,825,702
Covered: 1,364,428,763 out of 3,098,825,702

Uncovered: 2,714,811 out of 35,313,516
Matches: 27,953,394 out of 35,313,516
Mismatches: 4,350,173 out of 35,313,516
Insertions: 295,138 out of 35,313,516

Sus scrofa

Uncovered: 1,524,641,545 out of 2,808,526,148
Covered: 1,283,884,603 out of 2,808,526,148

Uncovered: 3,581,972 out of 29,865,122
Matches: 23,031,397 out of 29,865,122
Mismatches: 3,124,018 out of 29,865,122
Insertions: 127,735 out of 29,865,122