| Variant ID: vg0128509408 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28509408 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.72, T: 0.28, others allele: 0.00, population size: 47. )
CCGTTTTTCCCACGACACGCTCCTGTCAGGTGCCGTTGTACGGCGGTGCCAGATTGGGGTGTGACATATATGAACGATGGGAGGCGCGTGATGGTGGCGG[T/C]
GTCTAGGCCGAACCTGGGCAGCGTCGGCTGCTGCTGCTCCTGCTCCATGACCAGTGGACGATCACGCCGGCGACAGGCAATGCGGAGGGCTCGAGGGCAG
CTGCCCTCGAGCCCTCCGCATTGCCTGTCGCCGGCGTGATCGTCCACTGGTCATGGAGCAGGAGCAGCAGCAGCCGACGCTGCCCAGGTTCGGCCTAGAC[A/G]
CCGCCACCATCACGCGCCTCCCATCGTTCATATATGTCACACCCCAATCTGGCACCGCCGTACAACGGCACCTGACAGGAGCGTGTCGTGGGAAAAACGG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 25.20% | 3.90% | 13.03% | 57.96% | NA |
| All Indica | 2759 | 1.50% | 2.80% | 19.93% | 75.82% | NA |
| All Japonica | 1512 | 72.40% | 6.60% | 3.84% | 17.20% | NA |
| Aus | 269 | 4.50% | 0.00% | 0.00% | 95.54% | NA |
| Indica I | 595 | 1.70% | 1.50% | 9.24% | 87.56% | NA |
| Indica II | 465 | 1.90% | 3.90% | 7.74% | 86.45% | NA |
| Indica III | 913 | 0.70% | 3.20% | 40.85% | 55.31% | NA |
| Indica Intermediate | 786 | 2.00% | 2.50% | 10.94% | 84.48% | NA |
| Temperate Japonica | 767 | 93.00% | 0.00% | 0.13% | 6.91% | NA |
| Tropical Japonica | 504 | 33.30% | 18.70% | 10.32% | 37.70% | NA |
| Japonica Intermediate | 241 | 88.40% | 2.50% | 2.07% | 7.05% | NA |
| VI/Aromatic | 96 | 14.60% | 0.00% | 1.04% | 84.38% | NA |
| Intermediate | 90 | 31.10% | 6.70% | 7.78% | 54.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128509408 | T -> DEL | LOC_Os01g49570.1 | N | frameshift_variant | Average:21.776; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0128509408 | T -> C | LOC_Os01g49570.1 | missense_variant ; p.Thr56Ala; MODERATE | nonsynonymous_codon ; T56A | Average:21.776; most accessible tissue: Zhenshan97 panicle, score: 39.652 | unknown | unknown | TOLERATED | 1.00 |