| Variant ID: vg0128509396 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28509396 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.69, C: 0.31, others allele: 0.00, population size: 42. )
AAGCGGTTCGCGCCGTTTTTCCCACGACACGCTCCTGTCAGGTGCCGTTGTACGGCGGTGCCAGATTGGGGTGTGACATATATGAACGATGGGAGGCGCG[T/C]
GATGGTGGCGGTGTCTAGGCCGAACCTGGGCAGCGTCGGCTGCTGCTGCTCCTGCTCCATGACCAGTGGACGATCACGCCGGCGACAGGCAATGCGGAGG
CCTCCGCATTGCCTGTCGCCGGCGTGATCGTCCACTGGTCATGGAGCAGGAGCAGCAGCAGCCGACGCTGCCCAGGTTCGGCCTAGACACCGCCACCATC[A/G]
CGCGCCTCCCATCGTTCATATATGTCACACCCCAATCTGGCACCGCCGTACAACGGCACCTGACAGGAGCGTGTCGTGGGAAAAACGGCGCGAACCGCTT
| 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 | 25.10% | 1.70% | 9.90% | 63.35% | NA |
| All Indica | 2759 | 1.40% | 0.70% | 13.37% | 84.49% | NA |
| All Japonica | 1512 | 72.20% | 3.80% | 5.89% | 18.12% | NA |
| Aus | 269 | 4.50% | 0.00% | 0.00% | 95.54% | NA |
| Indica I | 595 | 1.80% | 0.00% | 5.04% | 93.11% | NA |
| Indica II | 465 | 1.90% | 1.50% | 3.23% | 93.33% | NA |
| Indica III | 913 | 0.70% | 0.80% | 30.78% | 67.80% | NA |
| Indica Intermediate | 786 | 1.80% | 0.60% | 5.47% | 92.11% | NA |
| Temperate Japonica | 767 | 92.80% | 0.00% | 0.13% | 7.04% | NA |
| Tropical Japonica | 504 | 32.90% | 10.90% | 16.07% | 40.08% | NA |
| Japonica Intermediate | 241 | 88.40% | 1.20% | 2.90% | 7.47% | NA |
| VI/Aromatic | 96 | 13.50% | 0.00% | 2.08% | 84.38% | NA |
| Intermediate | 90 | 31.10% | 3.30% | 8.89% | 56.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128509396 | T -> DEL | LOC_Os01g49570.1 | N | frameshift_variant | Average:21.721; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0128509396 | T -> C | LOC_Os01g49570.1 | missense_variant ; p.Thr60Ala; MODERATE | nonsynonymous_codon ; T60A | Average:21.721; most accessible tissue: Zhenshan97 panicle, score: 39.652 | unknown | unknown | TOLERATED | 1.00 |