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Human vs Rabbit LastZ alignments

Human (Homo sapiens, GRCh37) and Rabbit (Oryctolagus cuniculus, OryCun2.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 60. 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)3000
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)50
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 Rabbit
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: 2,036,094

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

Uncovered: 1,771,859,125 out of 3,098,825,702
Covered: 1,326,966,577 out of 3,098,825,702

Uncovered: 2,559,949 out of 35,313,516
Matches: 27,961,569 out of 35,313,516
Mismatches: 4,410,603 out of 35,313,516
Insertions: 381,395 out of 35,313,516

Oryctolagus cuniculus

Uncovered: 1,515,494,447 out of 2,737,473,256
Covered: 1,221,978,809 out of 2,737,473,256

Uncovered: 2,078,554 out of 29,964,475
Matches: 24,381,807 out of 29,964,475
Mismatches: 3,388,752 out of 29,964,475
Insertions: 115,362 out of 29,964,475