| Variant ID: vg1113572172 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 13572172 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, T: 0.03, others allele: 0.00, population size: 236. )
ACTAAATCATCGTAGCTCCGATTTGAGTGGTTCAAGTTGCTAAATTTTTCTAAAATCAAGATCTACATGTTAAAAATATCCACATGTACTGTTTATGCTT[G/T]
TTTTTGTACTGTTTTGTTGATCTTGTTCTTTTGCTTTAGTTTCCAACGTTCCTGAGGAGAGCGTTTTCGTTTAGGAAGGTTCAGAAGTGTTTGCGGAAGC
GCTTCCGCAAACACTTCTGAACCTTCCTAAACGAAAACGCTCTCCTCAGGAACGTTGGAAACTAAAGCAAAAGAACAAGATCAACAAAACAGTACAAAAA[C/A]
AAGCATAAACAGTACATGTGGATATTTTTAACATGTAGATCTTGATTTTAGAAAAATTTAGCAACTTGAACCACTCAAATCGGAGCTACGATGATTTAGT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 61.30% | 16.90% | 11.21% | 10.50% | NA |
| All Indica | 2759 | 38.40% | 26.10% | 18.01% | 17.43% | NA |
| All Japonica | 1512 | 95.60% | 1.90% | 1.92% | 0.66% | NA |
| Aus | 269 | 87.70% | 12.30% | 0.00% | 0.00% | NA |
| Indica I | 595 | 17.50% | 29.10% | 29.92% | 23.53% | NA |
| Indica II | 465 | 61.50% | 4.70% | 17.85% | 15.91% | NA |
| Indica III | 913 | 33.80% | 38.80% | 11.83% | 15.55% | NA |
| Indica Intermediate | 786 | 45.90% | 21.90% | 16.28% | 15.90% | NA |
| Temperate Japonica | 767 | 96.70% | 2.20% | 0.65% | 0.39% | NA |
| Tropical Japonica | 504 | 92.70% | 1.60% | 4.56% | 1.19% | NA |
| Japonica Intermediate | 241 | 97.90% | 1.20% | 0.41% | 0.41% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 71.10% | 18.90% | 4.44% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1113572172 | G -> T | LOC_Os11g23950.1 | downstream_gene_variant ; 4063.0bp to feature; MODIFIER | silent_mutation | Average:33.407; most accessible tissue: Zhenshan97 panicle, score: 43.098 | N | N | N | N |
| vg1113572172 | G -> T | LOC_Os11g23950-LOC_Os11g23970 | intergenic_region ; MODIFIER | silent_mutation | Average:33.407; most accessible tissue: Zhenshan97 panicle, score: 43.098 | N | N | N | N |
| vg1113572172 | G -> DEL | N | N | silent_mutation | Average:33.407; most accessible tissue: Zhenshan97 panicle, score: 43.098 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1113572172 | NA | 2.11E-06 | mr1550 | Ind_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 |
| vg1113572172 | 1.88E-06 | 1.20E-14 | mr1739 | 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 |
| vg1113572172 | NA | 1.65E-10 | mr1739 | Ind_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 |
| vg1113572172 | NA | 9.29E-06 | mr1759 | Ind_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 |
| vg1113572172 | NA | 1.09E-06 | mr1839 | Ind_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 |
| vg1113572172 | NA | 6.56E-06 | mr1909 | Ind_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 |
| vg1113572172 | NA | 8.34E-06 | mr1959 | Ind_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 |
| vg1113572172 | NA | 2.24E-06 | mr1378_2 | Ind_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 |
| vg1113572172 | NA | 1.06E-10 | mr1739_2 | 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 |