| Variant ID: vg1207459186 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 7459186 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TTGCGTACCTAACAAGATGACCGGAGTGCGGTTCCATTCTAGGTCTCGTTCCCCAGTCGACTGCTTGTGGCATGTCAACCGGGCCCTTATATTATTTTGT[C/T]
TTCCGTTGTTGTTTCTCTGATAGTTGTTGGCCTACCTGGCCTTAATGTAAGCATTTAACTCTCTTAGCCTAAATTCATTCGTGATATGTTGTGATTCGGC
GCCGAATCACAACATATCACGAATGAATTTAGGCTAAGAGAGTTAAATGCTTACATTAAGGCCAGGTAGGCCAACAACTATCAGAGAAACAACAACGGAA[G/A]
ACAAAATAATATAAGGGCCCGGTTGACATGCCACAAGCAGTCGACTGGGGAACGAGACCTAGAATGGAACCGCACTCCGGTCATCTTGTTAGGTACGCAA
| 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 | 63.60% | 1.90% | 29.48% | 4.95% | NA |
| All Indica | 2759 | 46.40% | 3.20% | 43.78% | 6.60% | NA |
| All Japonica | 1512 | 98.80% | 0.00% | 0.60% | 0.60% | NA |
| Aus | 269 | 30.10% | 0.70% | 55.39% | 13.75% | NA |
| Indica I | 595 | 31.40% | 2.40% | 49.92% | 16.30% | NA |
| Indica II | 465 | 73.50% | 2.80% | 22.37% | 1.29% | NA |
| Indica III | 913 | 41.80% | 4.10% | 49.95% | 4.16% | NA |
| Indica Intermediate | 786 | 46.90% | 3.20% | 44.66% | 5.22% | NA |
| Temperate Japonica | 767 | 99.50% | 0.00% | 0.39% | 0.13% | NA |
| Tropical Japonica | 504 | 98.00% | 0.00% | 0.79% | 1.19% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 0.83% | 0.83% | NA |
| VI/Aromatic | 96 | 82.30% | 0.00% | 13.54% | 4.17% | NA |
| Intermediate | 90 | 82.20% | 0.00% | 15.56% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1207459186 | C -> DEL | N | N | silent_mutation | Average:28.948; most accessible tissue: Minghui63 root, score: 57.225 | N | N | N | N |
| vg1207459186 | C -> T | LOC_Os12g13360.1 | downstream_gene_variant ; 2242.0bp to feature; MODIFIER | silent_mutation | Average:28.948; most accessible tissue: Minghui63 root, score: 57.225 | N | N | N | N |
| vg1207459186 | C -> T | LOC_Os12g13350-LOC_Os12g13360 | intergenic_region ; MODIFIER | silent_mutation | Average:28.948; most accessible tissue: Minghui63 root, score: 57.225 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1207459186 | NA | 1.20E-06 | mr1850 | 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 |
| vg1207459186 | NA | 1.96E-06 | mr1308_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 |
| vg1207459186 | NA | 1.73E-06 | mr1361_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 |
| vg1207459186 | 8.92E-06 | 8.92E-06 | mr1730_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 |
| vg1207459186 | 5.09E-06 | NA | mr1853_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 |
| vg1207459186 | 3.18E-07 | 3.18E-07 | mr1853_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 |