| Variant ID: vg0134084052 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 34084052 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CGGTGACGGTTTTTTTTGTTTCGATTTTTTATTTTCCCGTGCACACGTGAAAATCGCGATTTTCACAGACACTTCGTTCCAGACGGGTGGAAGATTCGCA[T/C]
GCTCGACCGCACAGAAAAATCATTATTGCACTAGTGGGAGTATATGTTAGCAGATTTGTTTCGAGCCTAATCAACTTTTATTATAGTTCGTGTGTGCGCC
GGCGCACACACGAACTATAATAAAAGTTGATTAGGCTCGAAACAAATCTGCTAACATATACTCCCACTAGTGCAATAATGATTTTTCTGTGCGGTCGAGC[A/G]
TGCGAATCTTCCACCCGTCTGGAACGAAGTGTCTGTGAAAATCGCGATTTTCACGTGTGCACGGGAAAATAAAAAATCGAAACAAAAAAAACCGTCACCG
| 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 | 91.00% | 6.70% | 2.33% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 72.20% | 20.70% | 7.08% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 60.00% | 29.50% | 10.56% | 0.00% | NA |
| Tropical Japonica | 504 | 93.10% | 5.00% | 1.98% | 0.00% | NA |
| Japonica Intermediate | 241 | 67.60% | 25.70% | 6.64% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 2.20% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0134084052 | T -> C | LOC_Os01g58960.1 | upstream_gene_variant ; 705.0bp to feature; MODIFIER | silent_mutation | Average:68.278; most accessible tissue: Zhenshan97 flower, score: 91.224 | N | N | N | N |
| vg0134084052 | T -> C | LOC_Os01g58950-LOC_Os01g58960 | intergenic_region ; MODIFIER | silent_mutation | Average:68.278; most accessible tissue: Zhenshan97 flower, score: 91.224 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0134084052 | NA | 1.08E-07 | mr1097 | 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 |
| vg0134084052 | 1.39E-06 | 1.39E-06 | mr1128 | Jap_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 |
| vg0134084052 | NA | 5.56E-06 | mr1530 | 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 |