| Variant ID: vg0129349785 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 29349785 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 28. )
ATTTGCACTTTGAACCACGCCATGCTATCAAGAGCCAGGCCCTCGCCGATTTTGTGGCAGAGTGGACCCCAGCTCCCGGGCCCGTCTCAGTCCCCGAGGC[T/C]
AGCTCGGGCCCCTCGCAGCTGCCTCACACGCCCACTGGGTGATGCAGTTCGACGGCTCCCTGTCTCTTCAGGGCGCCGGTGCGGGGGTCACGTTGACCTC
GAGGTCAACGTGACCCCCGCACCGGCGCCCTGAAGAGACAGGGAGCCGTCGAACTGCATCACCCAGTGGGCGTGTGAGGCAGCTGCGAGGGGCCCGAGCT[A/G]
GCCTCGGGGACTGAGACGGGCCCGGGAGCTGGGGTCCACTCTGCCACAAAATCGGCGAGGGCCTGGCTCTTGATAGCATGGCGTGGTTCAAAGTGCAAAT
| 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 | 41.10% | 20.80% | 26.30% | 11.81% | NA |
| All Indica | 2759 | 57.50% | 2.20% | 36.97% | 3.30% | NA |
| All Japonica | 1512 | 17.70% | 58.80% | 4.17% | 19.31% | NA |
| Aus | 269 | 9.70% | 3.70% | 42.75% | 43.87% | NA |
| Indica I | 595 | 34.50% | 2.20% | 58.99% | 4.37% | NA |
| Indica II | 465 | 49.50% | 1.70% | 45.38% | 3.44% | NA |
| Indica III | 913 | 79.40% | 2.50% | 15.88% | 2.19% | NA |
| Indica Intermediate | 786 | 54.30% | 2.20% | 39.82% | 3.69% | NA |
| Temperate Japonica | 767 | 2.30% | 92.00% | 0.13% | 5.48% | NA |
| Tropical Japonica | 504 | 35.90% | 14.70% | 10.32% | 39.09% | NA |
| Japonica Intermediate | 241 | 28.60% | 45.20% | 4.15% | 21.99% | NA |
| VI/Aromatic | 96 | 35.40% | 0.00% | 18.75% | 45.83% | NA |
| Intermediate | 90 | 28.90% | 26.70% | 30.00% | 14.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0129349785 | T -> DEL | N | N | silent_mutation | Average:16.63; most accessible tissue: Callus, score: 29.634 | N | N | N | N |
| vg0129349785 | T -> C | LOC_Os01g51080.1 | downstream_gene_variant ; 1561.0bp to feature; MODIFIER | silent_mutation | Average:16.63; most accessible tissue: Callus, score: 29.634 | N | N | N | N |
| vg0129349785 | T -> C | LOC_Os01g51100.1 | downstream_gene_variant ; 2898.0bp to feature; MODIFIER | silent_mutation | Average:16.63; most accessible tissue: Callus, score: 29.634 | N | N | N | N |
| vg0129349785 | T -> C | LOC_Os01g51090.1 | intron_variant ; MODIFIER | silent_mutation | Average:16.63; most accessible tissue: Callus, score: 29.634 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0129349785 | NA | 2.64E-06 | mr1011 | 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 |
| vg0129349785 | NA | 3.78E-13 | mr1013 | 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 |
| vg0129349785 | NA | 6.61E-15 | mr1031 | 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 |
| vg0129349785 | NA | 7.74E-06 | mr1031 | 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 |
| vg0129349785 | NA | 2.15E-12 | mr1034 | 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 |
| vg0129349785 | NA | 1.07E-15 | mr1056 | 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 |
| vg0129349785 | NA | 5.65E-06 | mr1056 | 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 |
| vg0129349785 | NA | 9.03E-06 | mr1277 | 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 |
| vg0129349785 | NA | 4.39E-07 | mr1291 | 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 |
| vg0129349785 | NA | 8.25E-10 | mr1232_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 |
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