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Human vs Platypus BlastZ alignments

Human (Homo sapiens, GRCh37) and Platypus (Ornithorhynchus anatinus, OANA5) 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)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
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 Platypus
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} {default_soft_masking => 1}

Results

Number of alignment blocks: 432,625

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

Uncovered: 2,932,774,374 out of 3,098,825,702
Covered: 166,051,328 out of 3,098,825,702

Uncovered: 9,877,146 out of 35,313,516
Matches: 19,012,420 out of 35,313,516
Mismatches: 6,069,477 out of 35,313,516
Insertions: 354,473 out of 35,313,516

Ornithorhynchus anatinus

Uncovered: 1,926,294,575 out of 2,073,148,626
Covered: 146,854,051 out of 2,073,148,626

Uncovered: 5,747,834 out of 24,997,756
Matches: 14,616,016 out of 24,997,756
Mismatches: 4,385,423 out of 24,997,756
Insertions: 248,483 out of 24,997,756