| Variant ID: vg1204640879 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 4640879 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CCGTTCGTCTTATTTAACAAATTTTAAAAATTAATTTTTCATATCATTTGATTCATGGTTAAATATATTTATATGTATATATATAGTTTTACATATTTTA[T/C]
AAAAGTTTTTGAATAAGACGAACGGTCAAACATATGCTAAAAAGTCAATGGTGTCAAATATTTAGAAACGGAGGGAGTAAGTATTTACCCCACTCAATTA
TAATTGAGTGGGGTAAATACTTACTCCCTCCGTTTCTAAATATTTGACACCATTGACTTTTTAGCATATGTTTGACCGTTCGTCTTATTCAAAAACTTTT[A/G]
TAAAATATGTAAAACTATATATATACATATAAATATATTTAACCATGAATCAAATGATATGAAAAATTAATTTTTAAAATTTGTTAAATAAGACGAACGG
| 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 | 86.30% | 12.00% | 1.69% | 0.00% | NA |
| All Indica | 2759 | 99.10% | 0.80% | 0.14% | 0.00% | NA |
| All Japonica | 1512 | 64.90% | 30.20% | 4.83% | 0.00% | NA |
| Aus | 269 | 71.70% | 28.30% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.60% | 0.30% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 98.50% | 1.10% | 0.38% | 0.00% | NA |
| Temperate Japonica | 767 | 55.40% | 36.60% | 7.95% | 0.00% | NA |
| Tropical Japonica | 504 | 89.10% | 9.10% | 1.79% | 0.00% | NA |
| Japonica Intermediate | 241 | 44.80% | 53.90% | 1.24% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 85.60% | 11.10% | 3.33% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1204640879 | T -> C | LOC_Os12g08900.1 | upstream_gene_variant ; 1331.0bp to feature; MODIFIER | silent_mutation | Average:44.2; most accessible tissue: Minghui63 root, score: 75.155 | N | N | N | N |
| vg1204640879 | T -> C | LOC_Os12g08890-LOC_Os12g08900 | intergenic_region ; MODIFIER | silent_mutation | Average:44.2; most accessible tissue: Minghui63 root, score: 75.155 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1204640879 | 4.74E-06 | NA | mr1691 | 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 |
| vg1204640879 | NA | 9.51E-06 | mr1691 | 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 |
| vg1204640879 | 1.61E-07 | NA | mr1693 | 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 |
| vg1204640879 | 3.52E-06 | 2.28E-08 | mr1693 | 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 |