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Human vs Pika BlastZ alignments

Human (Homo sapiens, GRCh37) and Pika (Ochotona princeps, pika) were aligned using the BlastZ alignment algorithm ( Schwartz S et al., Genome Res.;13(1):103-7, Kent WJ et al., Proc Natl Acad Sci U S A., 2003;100(20):11484-9 ) in Ensembl release 55. Human was used as the reference species. After running BlastZ, the raw BlastZ 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)
Gap extend penalty (E)
HSP threshold (K)
Threshold for gapped extension (L)
Threshold for alignments between gapped alignment blocks (H)
Masking count (M)
Seed and Transition value (T)
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Results

Number of alignment blocks: 1,430,719

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

Uncovered: 2,238,862,915 out of 3,098,825,702
Covered: 859,962,787 out of 3,098,825,702

Uncovered: 4,949,600 out of 35,313,516
Matches: 25,017,853 out of 35,313,516
Mismatches: 4,931,305 out of 35,313,516
Insertions: 414,758 out of 35,313,516

Ochotona princeps

Uncovered: 3,516,542,189 out of 4,294,967,295
Covered: 778,425,106 out of 4,294,967,295

Uncovered: 6,365,961 out of 26,499,928
Matches: 17,200,208 out of 26,499,928
Mismatches: 2,876,520 out of 26,499,928
Insertions: 57,239 out of 26,499,928