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Detailed information for vg0721993869:
| Variant ID: vg0721993869 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 21993869 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 124. )
Flanking Sequence (100 bp) in Reference Genome:
ACAACTGATTGTTTCTTGCTCCTCCAAGATACCAAATTGCCACCAATAAATACACAGTAGCCTGATGTTGACCTCCTATCATCAAGACAACTGCCCCAAT[C/A]
TGCATCACAATATCCCTCCACATCTAGGTGTCCATTCTTCTTGAACCATATGCCTTTACCTGGGCTTGCCTTCAAATATCTCAAAATTCTATACACAACA
Reverse complement sequence
TGTTGTGTATAGAATTTTGAGATATTTGAAGGCAAGCCCAGGTAAAGGCATATGGTTCAAGAAGAATGGACACCTAGATGTGGAGGGATATTGTGATGCA[G/T]
ATTGGGGCAGTTGTCTTGATGATAGGAGGTCAACATCAGGCTACTGTGTATTTATTGGTGGCAATTTGGTATCTTGGAGGAGCAAGAAACAATCAGTTGT
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 89.80% | 0.90% | 6.62% | 2.69% | NA |
| All Indica | 2759 | 93.40% | 0.90% | 5.51% | 0.22% | NA |
| All Japonica | 1512 | 82.70% | 1.10% | 8.27% | 7.94% | NA |
| Aus | 269 | 99.30% | 0.00% | 0.74% | 0.00% | NA |
| Indica I | 595 | 97.50% | 0.70% | 1.85% | 0.00% | NA |
| Indica II | 465 | 91.00% | 0.60% | 8.17% | 0.22% | NA |
| Indica III | 913 | 92.10% | 1.20% | 6.46% | 0.22% | NA |
| Indica Intermediate | 786 | 93.10% | 0.90% | 5.60% | 0.38% | NA |
| Temperate Japonica | 767 | 95.00% | 0.10% | 1.69% | 3.13% | NA |
| Tropical Japonica | 504 | 69.80% | 2.20% | 16.87% | 11.11% | NA |
| Japonica Intermediate | 241 | 70.10% | 2.10% | 11.20% | 16.60% | NA |
| VI/Aromatic | 96 | 70.80% | 2.10% | 27.08% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 0.00% | 8.89% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0721993869 | C -> DEL | LOC_Os07g36710.1 | N | frameshift_variant | Average:12.163; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0721993869 | C -> A | LOC_Os07g36710.1 | missense_variant ; p.Asp652Tyr; MODERATE | nonsynonymous_codon ; D652Y | Average:12.163; most accessible tissue: Minghui63 panicle, score: 20.733 | benign  |
1.161 |
DELETERIOUS | 0.00 |