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Human vs Panda LastZ alignments

Human (Homo sapiens, GRCh37) and Panda (Ailuropoda melanoleuca, ailMel1) 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 Panda
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: 2,018,327

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

Uncovered: 1,514,213,613 out of 3,098,825,702
Covered: 1,584,612,089 out of 3,098,825,702

Uncovered: 1,152,229 out of 35,313,516
Matches: 29,681,447 out of 35,313,516
Mismatches: 4,179,640 out of 35,313,516
Insertions: 300,200 out of 35,313,516

Ailuropoda melanoleuca

Uncovered: 801,810,329 out of 2,299,492,210
Covered: 1,497,681,881 out of 2,299,492,210

Uncovered: 979,586 out of 31,130,938
Matches: 26,654,196 out of 31,130,938
Mismatches: 3,370,793 out of 31,130,938
Insertions: 126,363 out of 31,130,938