| Variant ID: vg0330077379 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 30077379 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 241. )
AAAGTTTGGAACTAAATAAGGCCTTAAGTTAACTATAGAATTGGGATATTTTTTCTATAGGCTCACCAAAATTTGGCTTCAATCTGAAAGATACAAAATT[G/A]
AGATTACAAAATCCAAAAGATACAAAATACTACTGAGATTATCAAATATTGGTAAGACATATTTAGGCAACAAACCTAATCAGACCTTAAATTTTTTAGA
TCTAAAAAATTTAAGGTCTGATTAGGTTTGTTGCCTAAATATGTCTTACCAATATTTGATAATCTCAGTAGTATTTTGTATCTTTTGGATTTTGTAATCT[C/T]
AATTTTGTATCTTTCAGATTGAAGCCAAATTTTGGTGAGCCTATAGAAAAAATATCCCAATTCTATAGTTAACTTAAGGCCTTATTTAGTTCCAAACTTT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 92.70% | 5.40% | 1.90% | 0.00% | NA |
| All Indica | 2759 | 87.70% | 9.10% | 3.15% | 0.00% | NA |
| All Japonica | 1512 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 62.50% | 28.40% | 9.08% | 0.00% | NA |
| Indica II | 465 | 97.00% | 1.50% | 1.51% | 0.00% | NA |
| Indica III | 913 | 96.70% | 3.10% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 90.80% | 6.10% | 3.05% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.00% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 3.30% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0330077379 | G -> A | LOC_Os03g52390.1 | upstream_gene_variant ; 945.0bp to feature; MODIFIER | silent_mutation | Average:58.513; most accessible tissue: Zhenshan97 root, score: 84.5 | N | N | N | N |
| vg0330077379 | G -> A | LOC_Os03g52370.1 | downstream_gene_variant ; 1638.0bp to feature; MODIFIER | silent_mutation | Average:58.513; most accessible tissue: Zhenshan97 root, score: 84.5 | N | N | N | N |
| vg0330077379 | G -> A | LOC_Os03g52380.1 | downstream_gene_variant ; 334.0bp to feature; MODIFIER | silent_mutation | Average:58.513; most accessible tissue: Zhenshan97 root, score: 84.5 | N | N | N | N |
| vg0330077379 | G -> A | LOC_Os03g52400.1 | downstream_gene_variant ; 3192.0bp to feature; MODIFIER | silent_mutation | Average:58.513; most accessible tissue: Zhenshan97 root, score: 84.5 | N | N | N | N |
| vg0330077379 | G -> A | LOC_Os03g52410.1 | downstream_gene_variant ; 4953.0bp to feature; MODIFIER | silent_mutation | Average:58.513; most accessible tissue: Zhenshan97 root, score: 84.5 | N | N | N | N |
| vg0330077379 | G -> A | LOC_Os03g52370.2 | downstream_gene_variant ; 1638.0bp to feature; MODIFIER | silent_mutation | Average:58.513; most accessible tissue: Zhenshan97 root, score: 84.5 | N | N | N | N |
| vg0330077379 | G -> A | LOC_Os03g52380-LOC_Os03g52390 | intergenic_region ; MODIFIER | silent_mutation | Average:58.513; most accessible tissue: Zhenshan97 root, score: 84.5 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0330077379 | 2.59E-09 | 2.02E-17 | mr1038 | 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 |
| vg0330077379 | 3.06E-08 | 1.60E-16 | 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 |
| vg0330077379 | 2.38E-10 | 6.80E-20 | 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 |
| vg0330077379 | 7.48E-09 | 1.83E-17 | mr1389 | 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 |
| vg0330077379 | 9.37E-10 | 9.16E-21 | mr1038_2 | 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 |
| vg0330077379 | 6.55E-09 | 6.00E-19 | 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 |
| vg0330077379 | NA | 4.51E-06 | mr1283_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 |
| vg0330077379 | 6.06E-08 | 5.64E-17 | 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 |
| vg0330077379 | 3.73E-07 | 2.98E-16 | 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 |
| vg0330077379 | 7.74E-06 | 7.74E-06 | mr1529_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 |