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Human vs Mouse LastZ alignments

Human (Homo sapiens, GRCh37) and Mouse (Mus musculus, GRCm38) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 68. Human 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

Human Mouse
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}

Results

Number of alignment blocks: 1,488,960

Genome coverage (bp) Coding exon coverage (bp)
Homo sapiens

Uncovered: 2,118,013,527 out of 3,098,825,702
Covered: 980,812,175 out of 3,098,825,702

Uncovered: 1,388,922 out of 35,313,516
Matches: 28,035,486 out of 35,313,516
Mismatches: 5,482,646 out of 35,313,516
Insertions: 406,462 out of 35,313,516

Mus musculus

Uncovered: 1,832,305,590 out of 2,730,871,774
Covered: 898,566,184 out of 2,730,871,774

Uncovered: 4,064,323 out of 35,991,038
Matches: 26,773,881 out of 35,991,038
Mismatches: 4,974,151 out of 35,991,038
Insertions: 178,683 out of 35,991,038