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Human vs Wallaby BlastZ alignments

Human (Homo sapiens, GRCh37) and Wallaby (Macropus eugenii, Meug_1.0) 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 Wallaby
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: 578,119

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

Uncovered: 2,896,822,778 out of 3,098,825,702
Covered: 202,002,924 out of 3,098,825,702

Uncovered: 7,075,495 out of 35,313,516
Matches: 21,593,825 out of 35,313,516
Mismatches: 6,306,226 out of 35,313,516
Insertions: 337,970 out of 35,313,516

Macropus eugenii

Uncovered: 2,779,200,842 out of 2,955,773,937
Covered: 176,573,095 out of 2,955,773,937

Uncovered: 4,843,088 out of 25,589,509
Matches: 16,308,190 out of 25,589,509
Mismatches: 4,322,906 out of 25,589,509
Insertions: 115,325 out of 25,589,509