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Mouse vs Rat LastZ alignments

Mouse (Mus musculus, GRCm38) and Rat (Rattus norvegicus, Rnor_5.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 70. 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)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

Mouse Rat
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: 1,888,845

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

Uncovered: 799,027,022 out of 2,730,871,774
Covered: 1,931,844,752 out of 2,730,871,774

Uncovered: 340,510 out of 35,991,038
Matches: 32,847,949 out of 35,991,038
Mismatches: 2,681,750 out of 35,991,038
Insertions: 120,829 out of 35,991,038

Rattus norvegicus

Uncovered: 1,126,089,275 out of 2,909,698,938
Covered: 1,783,609,663 out of 2,909,698,938

Uncovered: 2,654,525 out of 34,224,882
Matches: 29,315,938 out of 34,224,882
Mismatches: 2,167,957 out of 34,224,882
Insertions: 86,462 out of 34,224,882