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Mouse vs Pig LastZ alignments

Mouse (Mus musculus, GRCm38) and Pig (Sus scrofa, Sscrofa10.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 68. Mouse 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

Mouse Pig
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: 1,170,013

Genome coverage (bp) Coding exon coverage (bp)
Mus musculus

Uncovered: 2,027,265,802 out of 2,730,871,774
Covered: 703,605,972 out of 2,730,871,774

Uncovered: 3,176,252 out of 35,991,038
Matches: 26,565,431 out of 35,991,038
Mismatches: 5,985,980 out of 35,991,038
Insertions: 263,375 out of 35,991,038

Sus scrofa

Uncovered: 2,115,947,372 out of 2,808,526,148
Covered: 692,578,776 out of 2,808,526,148

Uncovered: 4,021,908 out of 29,865,122
Matches: 21,299,411 out of 29,865,122
Mismatches: 4,307,689 out of 29,865,122
Insertions: 236,114 out of 29,865,122