| Variant ID: vg1003047386 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 3047386 |
| Reference Allele: C | Alternative Allele: T,A |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.71, C: 0.29, others allele: 0.00, population size: 245. )
TATTGACGCCTACTCTCATTGATCTCGTCCAAGAGGAACTGTTCGTCATCGCGAAATGCCATATGTTCCTAACATTAAATAATACAGAAAATGTAAATTA[C/T,A]
TACAAAAGGTGCATGGTATATTGTTATATCTACATTGTCAAATATGCATACACCCATGGGTTTATAATAGATAAAATCCCTTGTATGCTCTAAAAATTTC
GAAATTTTTAGAGCATACAAGGGATTTTATCTATTATAAACCCATGGGTGTATGCATATTTGACAATGTAGATATAACAATATACCATGCACCTTTTGTA[G/A,T]
TAATTTACATTTTCTGTATTATTTAATGTTAGGAACATATGGCATTTCGCGATGACGAACAGTTCCTCTTGGACGAGATCAATGAGAGTAGGCGTCAATA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 39.00% | 18.00% | 12.38% | 30.49% | A: 0.13% |
| All Indica | 2759 | 13.10% | 25.00% | 17.58% | 44.11% | A: 0.22% |
| All Japonica | 1512 | 93.70% | 0.80% | 1.79% | 3.77% | NA |
| Aus | 269 | 4.10% | 33.10% | 13.01% | 49.81% | NA |
| Indica I | 595 | 16.30% | 25.90% | 20.84% | 36.97% | NA |
| Indica II | 465 | 11.40% | 34.60% | 15.91% | 37.85% | A: 0.22% |
| Indica III | 913 | 7.60% | 22.80% | 16.10% | 53.01% | A: 0.55% |
| Indica Intermediate | 786 | 18.10% | 21.20% | 17.81% | 42.88% | NA |
| Temperate Japonica | 767 | 94.70% | 0.40% | 1.69% | 3.26% | NA |
| Tropical Japonica | 504 | 95.20% | 1.20% | 0.79% | 2.78% | NA |
| Japonica Intermediate | 241 | 87.10% | 1.20% | 4.15% | 7.47% | NA |
| VI/Aromatic | 96 | 15.60% | 45.80% | 23.96% | 14.58% | NA |
| Intermediate | 90 | 42.20% | 20.00% | 16.67% | 21.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1003047386 | C -> T | LOC_Os10g06010.1 | intron_variant ; MODIFIER | silent_mutation | Average:48.279; most accessible tissue: Zhenshan97 young leaf, score: 80.848 | N | N | N | N |
| vg1003047386 | C -> A | LOC_Os10g06010.1 | intron_variant ; MODIFIER | silent_mutation | Average:48.279; most accessible tissue: Zhenshan97 young leaf, score: 80.848 | N | N | N | N |
| vg1003047386 | C -> DEL | N | N | silent_mutation | Average:48.279; most accessible tissue: Zhenshan97 young leaf, score: 80.848 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1003047386 | NA | 8.93E-07 | mr1503 | 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 |
| vg1003047386 | NA | 5.37E-07 | mr1690 | 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 |
| vg1003047386 | 1.82E-07 | NA | mr1709 | 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 |
| vg1003047386 | 2.49E-07 | 6.97E-12 | mr1709 | 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 |
| vg1003047386 | 1.77E-13 | 5.82E-10 | mr1709_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 |
| vg1003047386 | 1.70E-13 | 4.89E-20 | mr1709_2 | Ind_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 |