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Mouse vs Dog LastZ alignments

Mouse (Mus musculus, GRCm38) and Dog (Canis lupus familiaris, CanFam3.1) 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 Dog
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: 1,249,618

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

Uncovered: 1,934,408,249 out of 2,730,871,774
Covered: 796,463,525 out of 2,730,871,774

Uncovered: 1,992,453 out of 35,991,038
Matches: 27,799,644 out of 35,991,038
Mismatches: 5,952,243 out of 35,991,038
Insertions: 246,698 out of 35,991,038

Canis lupus familiaris

Uncovered: 1,618,796,747 out of 2,410,960,148
Covered: 792,163,401 out of 2,410,960,148

Uncovered: 2,259,641 out of 33,014,761
Matches: 25,337,375 out of 33,014,761
Mismatches: 5,087,932 out of 33,014,761
Insertions: 329,813 out of 33,014,761