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Human vs Sheep LastZ alignments

Human (Homo sapiens, GRCh37) and Sheep (Ovis aries, Oar_v3.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 74. 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)
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 Sheep
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: 2,251,090

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

Uncovered: 1,718,913,064 out of 3,098,825,702
Covered: 1,379,912,638 out of 3,098,825,702

Uncovered: 1,763,067 out of 35,274,750
Matches: 28,597,970 out of 35,274,750
Mismatches: 4,512,216 out of 35,274,750
Insertions: 401,497 out of 35,274,750

Ovis aries

Uncovered: 1,314,417,060 out of 2,619,054,388
Covered: 1,304,637,328 out of 2,619,054,388

Uncovered: 2,399,326 out of 32,776,750
Matches: 26,362,035 out of 32,776,750
Mismatches: 3,841,546 out of 32,776,750
Insertions: 173,843 out of 32,776,750