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Human vs Guinea Pig BlastZ alignments

Human (Homo sapiens, GRCh37) and Guinea Pig (Cavia porcellus, cavPor3) 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: 1,861,036

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

Uncovered: 1,771,493,589 out of 3,098,825,702
Covered: 1,327,332,113 out of 3,098,825,702

Uncovered: 1,564,112 out of 35,313,516
Matches: 28,341,447 out of 35,313,516
Mismatches: 4,987,460 out of 35,313,516
Insertions: 420,497 out of 35,313,516

Cavia porcellus

Uncovered: 1,509,650,726 out of 2,723,219,641
Covered: 1,213,568,915 out of 2,723,219,641

Uncovered: 2,061,117 out of 29,810,634
Matches: 23,874,924 out of 29,810,634
Mismatches: 3,774,576 out of 29,810,634
Insertions: 100,017 out of 29,810,634