| Variant ID: vg0302880347 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 2880347 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: Unkown |
Inferred Ancestral Allele: Not determined.
TGACCGCAGAAGTACCTGCCGACGAGGCGGCGCCGGCGGCAAAGAAGCCGAGGGCGATGGGCGGACAATCGTTCAGCATGGCCGGCGCCGGCGCCGGCGG[C/G]
GAGCCGGCGAAGAAGTCGACGGCGATGAAGAGCCAATCCTTCAGCATGGCGGGCCAGCCGCAACAGTAGACGAAGAAGAAGAAGAAGAAGAAGAAGAAGA
TCTTCTTCTTCTTCTTCTTCTTCTTCTTCGTCTACTGTTGCGGCTGGCCCGCCATGCTGAAGGATTGGCTCTTCATCGCCGTCGACTTCTTCGCCGGCTC[G/C]
CCGCCGGCGCCGGCGCCGGCCATGCTGAACGATTGTCCGCCCATCGCCCTCGGCTTCTTTGCCGCCGGCGCCGCCTCGTCGGCAGGTACTTCTGCGGTCA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of Unkown(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 90.50% | 0.00% | 7.62% | 1.93% | NA |
| All Indica | 2759 | 92.80% | 0.00% | 5.15% | 2.07% | NA |
| All Japonica | 1512 | 84.10% | 0.00% | 14.02% | 1.92% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 86.90% | 0.00% | 11.60% | 1.51% | NA |
| Indica II | 465 | 92.30% | 0.00% | 4.30% | 3.44% | NA |
| Indica III | 913 | 96.10% | 0.00% | 1.97% | 1.97% | NA |
| Indica Intermediate | 786 | 93.80% | 0.00% | 4.45% | 1.78% | NA |
| Temperate Japonica | 767 | 80.60% | 0.00% | 17.86% | 1.56% | NA |
| Tropical Japonica | 504 | 86.50% | 0.00% | 11.11% | 2.38% | NA |
| Japonica Intermediate | 241 | 90.00% | 0.00% | 7.88% | 2.07% | NA |
| VI/Aromatic | 96 | 94.80% | 0.00% | 2.08% | 3.12% | NA |
| Intermediate | 90 | 94.40% | 0.00% | 3.33% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0302880347 | C -> G | LOC_Os03g05770.1 | synonymous_variant ; p.Gly464Gly; LOW | N | Average:69.431; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
| vg0302880347 | C -> G | LOC_Os03g05760.1 | downstream_gene_variant ; 4917.0bp to feature; MODIFIER | N | Average:69.431; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
| vg0302880347 | C -> G | LOC_Os03g05780.1 | downstream_gene_variant ; 2658.0bp to feature; MODIFIER | N | Average:69.431; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |