| Variant ID: vg0423388047 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 23388047 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GAGAGGAGGAAAACATGAAAAGAAACAGATATGTATGTATGATGCAGCGATAGGGTAGGCGTCCGATATTTCTGTTTTCATAAACTTCTAACTTTTTTTT[C/T]
CAAACTACCAACTTTCCTCAAACTTCTTCACAATTTCAGAAAGTAAACACAGCCTTAATTTATATTTTTCGACTTAATATGAGTGTTCGTATTTATGGTT
AACCATAAATACGAACACTCATATTAAGTCGAAAAATATAAATTAAGGCTGTGTTTACTTTCTGAAATTGTGAAGAAGTTTGAGGAAAGTTGGTAGTTTG[G/A]
AAAAAAAAGTTAGAAGTTTATGAAAACAGAAATATCGGACGCCTACCCTATCGCTGCATCATACATACATATCTGTTTCTTTTCATGTTTTCCTCCTCTC
| 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 | 83.20% | 14.80% | 2.01% | 0.00% | NA |
| All Indica | 2759 | 82.20% | 17.30% | 0.43% | 0.00% | NA |
| All Japonica | 1512 | 80.40% | 14.20% | 5.42% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 96.30% | 3.00% | 0.67% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 68.30% | 31.50% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 77.50% | 21.60% | 0.89% | 0.00% | NA |
| Temperate Japonica | 767 | 66.60% | 23.50% | 9.91% | 0.00% | NA |
| Tropical Japonica | 504 | 97.20% | 2.40% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 89.20% | 9.10% | 1.66% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 5.60% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0423388047 | C -> T | LOC_Os04g39300.1 | downstream_gene_variant ; 516.0bp to feature; MODIFIER | silent_mutation | Average:40.836; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| vg0423388047 | C -> T | LOC_Os04g39290-LOC_Os04g39300 | intergenic_region ; MODIFIER | silent_mutation | Average:40.836; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0423388047 | NA | 6.02E-07 | mr1037 | 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 |
| vg0423388047 | NA | 3.01E-07 | mr1585 | 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 |
| vg0423388047 | NA | 5.88E-06 | mr1439_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 |
| vg0423388047 | 4.11E-06 | NA | mr1695_2 | 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 |