| Variant ID: vg0630599588 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 30599588 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TATATATATATATATATATATATATATATATGTAAAATTGATCTGGAATGTGGCAGTTACATGGGCCTGAATGATGTGAGGAGAAAATTTGTTCTACTTG[C/G]
TAGGACATGATGTGATCTGGACAGGAAAACGGAAAACGTGGAGCAATTTGGGAGGGGGCGATATGGAGGAATCGGACCGGAAAATCGTAAAAAAATACGC
GCGTATTTTTTTACGATTTTCCGGTCCGATTCCTCCATATCGCCCCCTCCCAAATTGCTCCACGTTTTCCGTTTTCCTGTCCAGATCACATCATGTCCTA[G/C]
CAAGTAGAACAAATTTTCTCCTCACATCATTCAGGCCCATGTAACTGCCACATTCCAGATCAATTTTACATATATATATATATATATATATATATATATA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 81.90% | 1.90% | 1.18% | 15.02% | NA |
| All Indica | 2759 | 86.20% | 0.10% | 0.36% | 13.34% | NA |
| All Japonica | 1512 | 75.70% | 5.60% | 3.04% | 15.67% | NA |
| Aus | 269 | 74.30% | 0.00% | 0.00% | 25.65% | NA |
| Indica I | 595 | 99.70% | 0.00% | 0.00% | 0.34% | NA |
| Indica II | 465 | 83.70% | 0.00% | 0.22% | 16.13% | NA |
| Indica III | 913 | 77.70% | 0.20% | 0.77% | 21.36% | NA |
| Indica Intermediate | 786 | 87.40% | 0.10% | 0.25% | 12.21% | NA |
| Temperate Japonica | 767 | 96.00% | 1.30% | 1.30% | 1.43% | NA |
| Tropical Japonica | 504 | 47.60% | 13.30% | 5.36% | 33.73% | NA |
| Japonica Intermediate | 241 | 69.70% | 3.30% | 3.73% | 23.24% | NA |
| VI/Aromatic | 96 | 71.90% | 0.00% | 0.00% | 28.12% | NA |
| Intermediate | 90 | 88.90% | 1.10% | 0.00% | 10.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0630599588 | C -> G | LOC_Os06g50539.1 | upstream_gene_variant ; 632.0bp to feature; MODIFIER | silent_mutation | Average:55.351; most accessible tissue: Zhenshan97 flower, score: 81.047 | N | N | N | N |
| vg0630599588 | C -> G | LOC_Os06g50539.3 | upstream_gene_variant ; 632.0bp to feature; MODIFIER | silent_mutation | Average:55.351; most accessible tissue: Zhenshan97 flower, score: 81.047 | N | N | N | N |
| vg0630599588 | C -> G | LOC_Os06g50530.1 | downstream_gene_variant ; 1530.0bp to feature; MODIFIER | silent_mutation | Average:55.351; most accessible tissue: Zhenshan97 flower, score: 81.047 | N | N | N | N |
| vg0630599588 | C -> G | LOC_Os06g50530-LOC_Os06g50539 | intergenic_region ; MODIFIER | silent_mutation | Average:55.351; most accessible tissue: Zhenshan97 flower, score: 81.047 | N | N | N | N |
| vg0630599588 | C -> DEL | N | N | silent_mutation | Average:55.351; most accessible tissue: Zhenshan97 flower, score: 81.047 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0630599588 | 3.74E-07 | 1.23E-07 | mr1113 | Jap_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0630599588 | NA | 2.73E-07 | mr1414 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0630599588 | 8.35E-06 | 5.60E-07 | mr1682 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0630599588 | NA | 3.31E-06 | mr1850_2 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |