| Variant ID: vg0221475833 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 21475833 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.92, C: 0.07, others allele: 0.00, population size: 268. )
TCTTCTGATTTATTTGCCCTGTCATGGCATATCTGAACATCACCATAATCAGACCAACAAATCGTCAGCAAGTAAATCCTGCAAAAGGCAAAGCATGCTG[T/C]
ACAGTCTGATACGCGAGAAATCAATCATTCTCTCCCTTACTCTGGAGCATGGTATCCAAATGTTCCTAGCACCCTAGTCGAATGCAACCGGGCAGCGGTG
CACCGCTGCCCGGTTGCATTCGACTAGGGTGCTAGGAACATTTGGATACCATGCTCCAGAGTAAGGGAGAGAATGATTGATTTCTCGCGTATCAGACTGT[A/G]
CAGCATGCTTTGCCTTTTGCAGGATTTACTTGCTGACGATTTGTTGGTCTGATTATGGTGATGTTCAGATATGCCATGACAGGGCAAATAAATCAGAAGA
| 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 | 56.90% | 42.90% | 0.04% | 0.13% | NA |
| All Indica | 2759 | 92.50% | 7.20% | 0.07% | 0.14% | NA |
| All Japonica | 1512 | 3.60% | 96.40% | 0.00% | 0.07% | NA |
| Aus | 269 | 15.60% | 84.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.00% | 1.70% | 0.00% | 0.34% | NA |
| Indica II | 465 | 92.90% | 6.90% | 0.22% | 0.00% | NA |
| Indica III | 913 | 90.70% | 9.20% | 0.00% | 0.11% | NA |
| Indica Intermediate | 786 | 90.30% | 9.40% | 0.13% | 0.13% | NA |
| Temperate Japonica | 767 | 1.30% | 98.60% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 6.70% | 93.30% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 4.10% | 95.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 8.30% | 91.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 37.80% | 61.10% | 0.00% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0221475833 | T -> DEL | N | N | silent_mutation | Average:75.003; most accessible tissue: Zhenshan97 flag leaf, score: 84.585 | N | N | N | N |
| vg0221475833 | T -> C | LOC_Os02g35740.1 | upstream_gene_variant ; 4697.0bp to feature; MODIFIER | silent_mutation | Average:75.003; most accessible tissue: Zhenshan97 flag leaf, score: 84.585 | N | N | N | N |
| vg0221475833 | T -> C | LOC_Os02g35750.1 | downstream_gene_variant ; 2011.0bp to feature; MODIFIER | silent_mutation | Average:75.003; most accessible tissue: Zhenshan97 flag leaf, score: 84.585 | N | N | N | N |
| vg0221475833 | T -> C | LOC_Os02g35750.2 | downstream_gene_variant ; 365.0bp to feature; MODIFIER | silent_mutation | Average:75.003; most accessible tissue: Zhenshan97 flag leaf, score: 84.585 | N | N | N | N |
| vg0221475833 | T -> C | LOC_Os02g35750.3 | downstream_gene_variant ; 200.0bp to feature; MODIFIER | silent_mutation | Average:75.003; most accessible tissue: Zhenshan97 flag leaf, score: 84.585 | N | N | N | N |
| vg0221475833 | T -> C | LOC_Os02g35760.1 | intron_variant ; MODIFIER | silent_mutation | Average:75.003; most accessible tissue: Zhenshan97 flag leaf, score: 84.585 | N | N | N | N |
| vg0221475833 | T -> C | LOC_Os02g35760.2 | intron_variant ; MODIFIER | silent_mutation | Average:75.003; most accessible tissue: Zhenshan97 flag leaf, score: 84.585 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0221475833 | NA | 7.65E-15 | mr1156 | 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 |
| vg0221475833 | NA | 4.75E-11 | mr1720 | 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 |
| vg0221475833 | NA | 1.74E-12 | mr1914 | 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 |
| vg0221475833 | 3.32E-06 | 3.32E-06 | mr1918 | 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 |
| vg0221475833 | NA | 1.53E-30 | mr1037_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 |
| vg0221475833 | NA | 1.22E-56 | mr1109_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 |
| vg0221475833 | NA | 1.68E-44 | mr1509_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 |
| vg0221475833 | NA | 5.77E-13 | mr1514_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 |
| vg0221475833 | NA | 5.75E-16 | mr1720_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 |
| vg0221475833 | NA | 1.59E-06 | mr1911_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 |