| Variant ID: vg0318823675 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 18823675 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TGATTGATATAACAATAATTTTGATGATTAATGATGACGGAGGCACAATTTGTACAATACTGATGAATTTATGCTATGCTTGATATCTTAACTTAGTTCC[T/C]
GATTTCTTAAAAGTTTTTGTCAAACCTTGTTGATCCTAAAACCCACAAAAGTTGTTAAAAAACTTTCAGTCCTCATTGACTAAGCCAAGAAATCAAACAG
CTGTTTGATTTCTTGGCTTAGTCAATGAGGACTGAAAGTTTTTTAACAACTTTTGTGGGTTTTAGGATCAACAAGGTTTGACAAAAACTTTTAAGAAATC[A/G]
GGAACTAAGTTAAGATATCAAGCATAGCATAAATTCATCAGTATTGTACAAATTGTGCCTCCGTCATCATTAATCATCAAAATTATTGTTATATCAATCA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 85.30% | 3.10% | 4.36% | 7.26% | NA |
| All Indica | 2759 | 79.50% | 5.30% | 6.74% | 8.48% | NA |
| All Japonica | 1512 | 98.50% | 0.00% | 0.07% | 1.39% | NA |
| Aus | 269 | 70.30% | 0.40% | 5.58% | 23.79% | NA |
| Indica I | 595 | 70.80% | 5.40% | 6.55% | 17.31% | NA |
| Indica II | 465 | 59.80% | 11.60% | 18.92% | 9.68% | NA |
| Indica III | 913 | 95.20% | 1.90% | 0.99% | 1.97% | NA |
| Indica Intermediate | 786 | 79.60% | 5.30% | 6.36% | 8.65% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.00% | 0.00% | 0.40% | NA |
| Japonica Intermediate | 241 | 92.10% | 0.00% | 0.00% | 7.88% | NA |
| VI/Aromatic | 96 | 80.20% | 0.00% | 2.08% | 17.71% | NA |
| Intermediate | 90 | 90.00% | 0.00% | 2.22% | 7.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0318823675 | T -> C | LOC_Os03g32910.1 | downstream_gene_variant ; 94.0bp to feature; MODIFIER | silent_mutation | Average:14.549; most accessible tissue: Minghui63 root, score: 25.504 | N | N | N | N |
| vg0318823675 | T -> C | LOC_Os03g32920.1 | downstream_gene_variant ; 1468.0bp to feature; MODIFIER | silent_mutation | Average:14.549; most accessible tissue: Minghui63 root, score: 25.504 | N | N | N | N |
| vg0318823675 | T -> C | LOC_Os03g32930.1 | downstream_gene_variant ; 3450.0bp to feature; MODIFIER | silent_mutation | Average:14.549; most accessible tissue: Minghui63 root, score: 25.504 | N | N | N | N |
| vg0318823675 | T -> C | LOC_Os03g32910-LOC_Os03g32920 | intergenic_region ; MODIFIER | silent_mutation | Average:14.549; most accessible tissue: Minghui63 root, score: 25.504 | N | N | N | N |
| vg0318823675 | T -> DEL | N | N | silent_mutation | Average:14.549; most accessible tissue: Minghui63 root, score: 25.504 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0318823675 | 9.64E-06 | NA | mr1352_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 |
| vg0318823675 | 1.95E-06 | NA | mr1352_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 |
| vg0318823675 | 4.09E-06 | NA | mr1671_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 |