| Variant ID: vg0817362014 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17362014 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CAACAGATTTAAACACAGTGTTATTAGTTTCATGTTTAACCAAAATGTCACCACTTACTAGCACTAATACCTAACACAGTAGGAGGATGTTTAGTATGAT[C/G]
AGCATAAGGATTAAAACCTAAACCACGGTTATGTGTGCTAACCTTAGATTGATCTAGAATCATGTTGAGGTTCTTTTTACCATCAGAAAATCTTAGCAAA
TTTGCTAAGATTTTCTGATGGTAAAAAGAACCTCAACATGATTCTAGATCAATCTAAGGTTAGCACACATAACCGTGGTTTAGGTTTTAATCCTTATGCT[G/C]
ATCATACTAAACATCCTCCTACTGTGTTAGGTATTAGTGCTAGTAAGTGGTGACATTTTGGTTAAACATGAAACTAATAACACTGTGTTTAAATCTGTTG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 35.10% | 6.40% | 0.57% | 57.89% | NA |
| All Indica | 2759 | 3.60% | 7.00% | 0.80% | 88.66% | NA |
| All Japonica | 1512 | 94.00% | 2.10% | 0.20% | 3.70% | NA |
| Aus | 269 | 0.40% | 27.50% | 0.00% | 72.12% | NA |
| Indica I | 595 | 6.90% | 3.00% | 1.01% | 89.08% | NA |
| Indica II | 465 | 3.40% | 6.00% | 0.86% | 89.68% | NA |
| Indica III | 913 | 1.10% | 13.40% | 0.55% | 84.99% | NA |
| Indica Intermediate | 786 | 4.10% | 3.10% | 0.89% | 91.98% | NA |
| Temperate Japonica | 767 | 95.30% | 3.70% | 0.13% | 0.91% | NA |
| Tropical Japonica | 504 | 90.70% | 0.80% | 0.40% | 8.13% | NA |
| Japonica Intermediate | 241 | 96.70% | 0.00% | 0.00% | 3.32% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 0.00% | 7.29% | NA |
| Intermediate | 90 | 54.40% | 6.70% | 2.22% | 36.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817362014 | C -> G | LOC_Os08g28450.1 | intron_variant ; MODIFIER | silent_mutation | Average:7.615; most accessible tissue: Callus, score: 27.507 | N | N | N | N |
| vg0817362014 | C -> DEL | N | N | silent_mutation | Average:7.615; most accessible tissue: Callus, score: 27.507 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0817362014 | 2.88E-06 | NA | mr1040 | 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 |
| vg0817362014 | 8.57E-07 | 1.23E-08 | mr1836 | 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 |
| vg0817362014 | 6.27E-06 | NA | mr1113_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 |
| vg0817362014 | 7.28E-06 | NA | mr1247_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 |