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Human vs Shrew BlastZ alignments

Human (Homo sapiens, GRCh37) and Shrew (Sorex araneus, COMMON_SHREW1) 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)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 Shrew
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: 1,229,844

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

Uncovered: 2,465,414,385 out of 3,098,825,702
Covered: 633,411,317 out of 3,098,825,702

Uncovered: 9,102,296 out of 35,313,516
Matches: 21,143,712 out of 35,313,516
Mismatches: 4,712,512 out of 35,313,516
Insertions: 354,996 out of 35,313,516

Sorex araneus

Uncovered: 2,363,501,526 out of 2,944,193,050
Covered: 580,691,524 out of 2,944,193,050

Uncovered: 3,983,955 out of 20,841,358
Matches: 14,278,600 out of 20,841,358
Mismatches: 2,533,255 out of 20,841,358
Insertions: 45,548 out of 20,841,358