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Human vs Dog LastZ alignments

Human (Homo sapiens, GRCh37) and Dog (Canis lupus familiaris, CanFam3.1) 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 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}

Results

Number of alignment blocks: 2,113,078

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

Uncovered: 1,563,293,816 out of 3,098,825,702
Covered: 1,535,531,886 out of 3,098,825,702

Uncovered: 1,152,109 out of 35,313,516
Matches: 29,615,216 out of 35,313,516
Mismatches: 4,248,393 out of 35,313,516
Insertions: 297,798 out of 35,313,516

Canis lupus familiaris

Uncovered: 956,419,600 out of 2,410,960,148
Covered: 1,454,540,548 out of 2,410,960,148

Uncovered: 1,599,668 out of 33,014,761
Matches: 27,550,553 out of 33,014,761
Mismatches: 3,674,737 out of 33,014,761
Insertions: 189,803 out of 33,014,761