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Cow vs Sheep LastZ alignments

Cow (Bos taurus, UMD3.1) and Sheep (Ovis aries, Oar_v3.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 74. Cow 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

Cow 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} {default_soft_masking => 1}

Results

Number of alignment blocks: 1,232,108

Genome coverage (bp) Coding exon coverage (bp)
Bos taurus

Uncovered: 353,517,549 out of 2,670,422,299
Covered: 2,316,904,750 out of 2,670,422,299

Uncovered: 714,102 out of 32,345,388
Matches: 30,320,433 out of 32,345,388
Mismatches: 1,177,310 out of 32,345,388
Insertions: 133,543 out of 32,345,388

Ovis aries

Uncovered: 385,598,737 out of 2,619,054,388
Covered: 2,233,455,651 out of 2,619,054,388

Uncovered: 1,242,566 out of 32,776,750
Matches: 30,461,254 out of 32,776,750
Mismatches: 1,016,818 out of 32,776,750
Insertions: 56,112 out of 32,776,750