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Dog vs Horse LastZ alignments

Dog (Canis lupus familiaris, CanFam3.1) and Horse (Equus caballus, EquCab2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 68. Dog 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

Dog Horse
Chunk size 10,000,000 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: 1,952,527

Genome coverage (bp) Coding exon coverage (bp)
Canis lupus familiaris

Uncovered: 653,781,715 out of 2,410,960,148
Covered: 1,757,178,433 out of 2,410,960,148

Uncovered: 1,071,519 out of 33,014,761
Matches: 28,444,980 out of 33,014,761
Mismatches: 3,336,940 out of 33,014,761
Insertions: 161,322 out of 33,014,761

Equus caballus

Uncovered: 752,150,388 out of 2,474,912,402
Covered: 1,722,762,014 out of 2,474,912,402

Uncovered: 2,991,284 out of 31,526,203
Matches: 25,687,654 out of 31,526,203
Mismatches: 2,735,857 out of 31,526,203
Insertions: 111,408 out of 31,526,203