| Variant ID: vg0615907055 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 15907055 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 340. )
ACCACAATTGCAGGAGGCAGATATCGAGTTCCCTTCTTTGGTACAACTGGAAGAGTTCCTTAAAATCTACAAATCATGTATTATTGGGGTGGTGAAAATC[C/G]
ACGTTGGTGTAGTAGGCACCGAACATCCCAACACCCTTTTTGGCCTCCTCCAAATACCATTCATGCAGCCAATGCGCTTGAGTTCCTAAGGATTCAATTT
AAATTGAATCCTTAGGAACTCAAGCGCATTGGCTGCATGAATGGTATTTGGAGGAGGCCAAAAAGGGTGTTGGGATGTTCGGTGCCTACTACACCAACGT[G/C]
GATTTTCACCACCCCAATAATACATGATTTGTAGATTTTAAGGAACTCTTCCAGTTGTACCAAAGAAGGGAACTCGATATCTGCCTCCTGCAATTGTGGT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 92.00% | 7.70% | 0.32% | 0.00% | NA |
| All Indica | 2759 | 87.10% | 12.40% | 0.51% | 0.00% | NA |
| All Japonica | 1512 | 99.10% | 0.80% | 0.07% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.70% | 0.00% | 0.34% | 0.00% | NA |
| Indica II | 465 | 88.00% | 11.60% | 0.43% | 0.00% | NA |
| Indica III | 913 | 75.40% | 24.10% | 0.55% | 0.00% | NA |
| Indica Intermediate | 786 | 90.80% | 8.50% | 0.64% | 0.00% | NA |
| Temperate Japonica | 767 | 98.60% | 1.30% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 10.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0615907055 | C -> G | LOC_Os06g28040.1 | upstream_gene_variant ; 3801.0bp to feature; MODIFIER | silent_mutation | Average:36.295; most accessible tissue: Zhenshan97 young leaf, score: 63.653 | N | N | N | N |
| vg0615907055 | C -> G | LOC_Os06g28010.1 | downstream_gene_variant ; 4980.0bp to feature; MODIFIER | silent_mutation | Average:36.295; most accessible tissue: Zhenshan97 young leaf, score: 63.653 | N | N | N | N |
| vg0615907055 | C -> G | LOC_Os06g28020.1 | downstream_gene_variant ; 1367.0bp to feature; MODIFIER | silent_mutation | Average:36.295; most accessible tissue: Zhenshan97 young leaf, score: 63.653 | N | N | N | N |
| vg0615907055 | C -> G | LOC_Os06g28030.1 | intron_variant ; MODIFIER | silent_mutation | Average:36.295; most accessible tissue: Zhenshan97 young leaf, score: 63.653 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0615907055 | 1.64E-08 | NA | mr1068 | 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 |
| vg0615907055 | 1.60E-07 | NA | mr1068 | 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 |
| vg0615907055 | 2.84E-08 | NA | mr1090 | 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 |
| vg0615907055 | 8.76E-08 | 5.44E-10 | mr1090 | 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 |
| vg0615907055 | 4.29E-06 | NA | mr1094 | 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 |
| vg0615907055 | 1.15E-06 | NA | mr1096 | 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 |
| vg0615907055 | 1.11E-06 | NA | mr1110 | 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 |
| vg0615907055 | 2.55E-08 | NA | mr1111 | 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 |
| vg0615907055 | 7.22E-06 | NA | mr1111 | 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 |
| vg0615907055 | 1.37E-09 | NA | mr1121 | 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 |
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