| Variant ID: vg1214763416 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 14763416 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.80, C: 0.20, others allele: 0.00, population size: 35. )
GACTGCTGCCAAGTGAACACGTCAGCATTGTCATGGAGGAAGGTGATGAGCGCGAGTTCCTATTTCTCTCCTAGTGATGCCCCGATCTTAACGGTCTTGT[T/C]
GGGGTTGGCACTGAAGAGTGGAACGATATTGATTGCGCCGTCTGGTTTTGGCGTCTTGTTTGTCTTGCTCACTTTCTTGGGTGGCTCTGCTGTGGCAGGC
GCCTGCCACAGCAGAGCCACCCAAGAAAGTGAGCAAGACAAACAAGACGCCAAAACCAGACGGCGCAATCAATATCGTTCCACTCTTCAGTGCCAACCCC[A/G]
ACAAGACCGTTAAGATCGGGGCATCACTAGGAGAGAAATAGGAACTCGCGCTCATCACCTTCCTCCATGACAATGCTGACGTGTTCACTTGGCAGCAGTC
| 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 | 32.90% | 2.30% | 62.65% | 2.16% | NA |
| All Indica | 2759 | 16.70% | 2.80% | 79.56% | 0.94% | NA |
| All Japonica | 1512 | 67.70% | 1.80% | 27.05% | 3.44% | NA |
| Aus | 269 | 12.60% | 0.40% | 82.53% | 4.46% | NA |
| Indica I | 595 | 17.10% | 1.00% | 80.50% | 1.34% | NA |
| Indica II | 465 | 17.20% | 1.30% | 79.57% | 1.94% | NA |
| Indica III | 913 | 15.40% | 4.70% | 79.85% | 0.00% | NA |
| Indica Intermediate | 786 | 17.40% | 2.90% | 78.50% | 1.15% | NA |
| Temperate Japonica | 767 | 89.00% | 0.40% | 8.74% | 1.83% | NA |
| Tropical Japonica | 504 | 39.90% | 3.20% | 51.79% | 5.16% | NA |
| Japonica Intermediate | 241 | 58.10% | 3.30% | 33.61% | 4.98% | NA |
| VI/Aromatic | 96 | 1.00% | 1.00% | 87.50% | 10.42% | NA |
| Intermediate | 90 | 40.00% | 1.10% | 56.67% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1214763416 | T -> C | LOC_Os12g25500.1 | downstream_gene_variant ; 1897.0bp to feature; MODIFIER | silent_mutation | Average:24.923; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 | N | N | N | N |
| vg1214763416 | T -> C | LOC_Os12g25510.1 | intron_variant ; MODIFIER | silent_mutation | Average:24.923; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 | N | N | N | N |
| vg1214763416 | T -> DEL | N | N | silent_mutation | Average:24.923; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1214763416 | NA | 1.70E-06 | mr1094 | 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 |
| vg1214763416 | NA | 9.12E-07 | mr1096 | 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 |
| vg1214763416 | 7.53E-06 | 1.20E-08 | mr1111 | 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 |
| vg1214763416 | NA | 1.89E-06 | mr1211 | 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 |
| vg1214763416 | 5.66E-06 | 5.65E-06 | mr1407_2 | 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 |
| vg1214763416 | NA | 1.29E-06 | mr1554_2 | 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 |