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Human vs Cow LastZ alignments

Human (Homo sapiens, GRCh37) and Cow (Bos taurus, UMD3.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 64. 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)3000
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
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

Human Cow
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: 2,240,708

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

Uncovered: 1,698,219,231 out of 3,098,825,702
Covered: 1,400,606,471 out of 3,098,825,702

Uncovered: 994,019 out of 35,313,516
Matches: 29,508,826 out of 35,313,516
Mismatches: 4,503,977 out of 35,313,516
Insertions: 306,694 out of 35,313,516

Bos taurus

Uncovered: 1,347,961,612 out of 2,670,422,299
Covered: 1,322,460,687 out of 2,670,422,299

Uncovered: 1,879,091 out of 32,345,388
Matches: 26,595,507 out of 32,345,388
Mismatches: 3,735,661 out of 32,345,388
Insertions: 135,129 out of 32,345,388