| Variant ID: vg1207361973 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 7361973 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 117. )
GGGACAGTAGAGGTGGGCCGCTGAAGGTGATAGCTCAGTACGGGTATTCCTCCATGTTAGTATATATTCCTAAGACAAATTCCTGGGGAGGTTACTCTTC[C/T]
GTATTTAGCCCCGGTTGAACGGCCATGACAGGTTGTCGTAAGGAACTCGGCAACCCAGGGTGGTCTCTTGAAACACCAGGAGGACACTGTTAAGGGGTGT
ACACCCCTTAACAGTGTCCTCCTGGTGTTTCAAGAGACCACCCTGGGTTGCCGAGTTCCTTACGACAACCTGTCATGGCCGTTCAACCGGGGCTAAATAC[G/A]
GAAGAGTAACCTCCCCAGGAATTTGTCTTAGGAATATATACTAACATGGAGGAATACCCGTACTGAGCTATCACCTTCAGCGGCCCACCTCTACTGTCCC
| 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 | 76.30% | 3.00% | 3.70% | 17.03% | NA |
| All Indica | 2759 | 66.10% | 4.90% | 5.76% | 23.20% | NA |
| All Japonica | 1512 | 99.50% | 0.10% | 0.07% | 0.40% | NA |
| Aus | 269 | 45.70% | 0.00% | 3.72% | 50.56% | NA |
| Indica I | 595 | 54.10% | 6.10% | 16.47% | 23.36% | NA |
| Indica II | 465 | 50.10% | 11.40% | 4.30% | 34.19% | NA |
| Indica III | 913 | 87.50% | 0.10% | 0.55% | 11.83% | NA |
| Indica Intermediate | 786 | 59.80% | 5.90% | 4.58% | 29.77% | NA |
| Temperate Japonica | 767 | 99.20% | 0.10% | 0.13% | 0.52% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 77.10% | 0.00% | 2.08% | 20.83% | NA |
| Intermediate | 90 | 90.00% | 3.30% | 3.33% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1207361973 | C -> DEL | N | N | silent_mutation | Average:61.21; most accessible tissue: Minghui63 flag leaf, score: 80.516 | N | N | N | N |
| vg1207361973 | C -> T | LOC_Os12g13209.1 | upstream_gene_variant ; 2424.0bp to feature; MODIFIER | silent_mutation | Average:61.21; most accessible tissue: Minghui63 flag leaf, score: 80.516 | N | N | N | N |
| vg1207361973 | C -> T | LOC_Os12g13220.1 | upstream_gene_variant ; 1458.0bp to feature; MODIFIER | silent_mutation | Average:61.21; most accessible tissue: Minghui63 flag leaf, score: 80.516 | N | N | N | N |
| vg1207361973 | C -> T | LOC_Os12g13230.1 | downstream_gene_variant ; 2825.0bp to feature; MODIFIER | silent_mutation | Average:61.21; most accessible tissue: Minghui63 flag leaf, score: 80.516 | N | N | N | N |
| vg1207361973 | C -> T | LOC_Os12g13209-LOC_Os12g13220 | intergenic_region ; MODIFIER | silent_mutation | Average:61.21; most accessible tissue: Minghui63 flag leaf, score: 80.516 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1207361973 | 1.64E-06 | 2.78E-07 | mr1038 | 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 |
| vg1207361973 | 5.46E-07 | 1.60E-08 | mr1038 | 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 |
| vg1207361973 | NA | 3.31E-10 | mr1141 | 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 |
| vg1207361973 | 7.30E-10 | 2.19E-11 | mr1389 | 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 |
| vg1207361973 | 1.31E-09 | 2.13E-11 | mr1389 | Ind_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 |
| vg1207361973 | 3.14E-06 | 1.32E-09 | mr1038_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 |
| vg1207361973 | 1.40E-06 | 8.12E-10 | mr1038_2 | 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 |
| vg1207361973 | 1.57E-06 | 1.21E-12 | mr1141_2 | 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 |
| vg1207361973 | NA | 2.94E-06 | mr1268_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 |
| vg1207361973 | NA | 2.14E-06 | mr1268_2 | 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 |
| vg1207361973 | 7.15E-08 | 8.02E-11 | mr1389_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 |
| vg1207361973 | 1.00E-08 | 4.36E-12 | mr1389_2 | 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 |