Arabidopsis thaliana vs Oryza glaberrima BlastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Oryza glaberrima (Oryza glaberrima, AGI1.1) 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 Plants release 76. Arabidopsis thaliana 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.

Results

Number of alignment blocks: 75,700

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 94,170,882 out of 119,667,750
Covered: 25,496,868 out of 119,667,750

Uncovered: 14,343,218 out of 33,462,323
Matches: 12,470,076 out of 33,462,323
Mismatches: 6,291,046 out of 33,462,323
Insertions: 357,983 out of 33,462,323

Oryza glaberrima

Uncovered: 298,628,890 out of 316,419,574
Covered: 17,790,684 out of 316,419,574

Uncovered: 24,105,752 out of 36,293,721
Matches: 7,919,959 out of 36,293,721
Mismatches: 3,976,811 out of 36,293,721
Insertions: 291,199 out of 36,293,721

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
Other parameters (other)