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Pig vs Sheep LastZ alignments

Pig (Sus scrofa, Sscrofa10.2) and Sheep (Ovis aries, Oar_v3.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 74. 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.

Configuration parameters

ParameterValue
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)10
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

Pig 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: 2,612,774

Genome coverage (bp) Coding exon coverage (bp)
Sus scrofa

Uncovered: 1,208,279,637 out of 2,808,525,991
Covered: 1,600,246,354 out of 2,808,525,991

Uncovered: 918,263 out of 29,865,122
Matches: 25,696,409 out of 29,865,122
Mismatches: 3,033,061 out of 29,865,122
Insertions: 217,389 out of 29,865,122

Ovis aries

Uncovered: 1,253,305,322 out of 2,619,054,388
Covered: 1,365,749,066 out of 2,619,054,388

Uncovered: 4,637,819 out of 32,776,750
Matches: 25,101,190 out of 32,776,750
Mismatches: 2,890,624 out of 32,776,750
Insertions: 147,117 out of 32,776,750