| Variant ID: vg0432486247 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 32486247 |
| Reference Allele: T | Alternative Allele: C,TACAAGTTTTTTCTGCATACTTTGTCCTCACTCATGTGCACTCGGGGAGAATTTCCCAATCGGTCACTCATCCCCCCTTATAGACC |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.74, T: 0.27, others allele: 0.00, population size: 200. )
AAGTTTTTTTGGAACTAAATAGGTGTAACGTCCCGCTTCTCTTAGGCCAGGCCCACTTACATCTGGCAGCTTTCATAGGTCATAGACTGCCCTTACAGAC[T/C,TACAAGTTTTTTCTGCATACTTTGTCCTCACTCATGTGCACTCGGGGAGAATTTCCCAATCGGTCACTCATCCCCCCTTATAGACC]
AACACAAGTTTTTTCTGCATACTTTGTCCTCACTCATGTGCACTCGGGGAGAATTTCCCGATCGGTCACTCATCCCCCCTTACAGACCAACACAAGTTTT
AAAACTTGTGTTGGTCTGTAAGGGGGGATGAGTGACCGATCGGGAAATTCTCCCCGAGTGCACATGAGTGAGGACAAAGTATGCAGAAAAAACTTGTGTT[A/G,GGTCTATAAGGGGGGATGAGTGACCGATTGGGAAATTCTCCCCGAGTGCACATGAGTGAGGACAAAGTATGCAGAAAAAACTTGTA]
GTCTGTAAGGGCAGTCTATGACCTATGAAAGCTGCCAGATGTAAGTGGGCCTGGCCTAAGAGAAGCGGGACGTTACACCTATTTAGTTCCAAAAAAACTT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 92.10% | 5.90% | 0.44% | 1.52% | TACAAGTTTTTTCTGCATACTTTGTCCTCACTCATGTGCACTCGGGGAGAATTTCCCAATCGGTCACTCATCCCCCCTTATAGACC: 0.02% |
| All Indica | 2759 | 90.90% | 7.40% | 0.25% | 1.49% | NA |
| All Japonica | 1512 | 98.30% | 1.60% | 0.13% | 0.00% | NA |
| Aus | 269 | 75.80% | 14.90% | 2.97% | 5.95% | TACAAGTTTTTTCTGCATACTTTGTCCTCACTCATGTGCACTCGGGGAGAATTTCCCAATCGGTCACTCATCCCCCCTTATAGACC: 0.37% |
| Indica I | 595 | 98.70% | 1.20% | 0.17% | 0.00% | NA |
| Indica II | 465 | 89.70% | 9.50% | 0.00% | 0.86% | NA |
| Indica III | 913 | 85.30% | 12.70% | 0.22% | 1.75% | NA |
| Indica Intermediate | 786 | 92.20% | 4.60% | 0.51% | 2.67% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 95.60% | 4.20% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 1.20% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 82.30% | 5.20% | 1.04% | 11.46% | NA |
| Intermediate | 90 | 86.70% | 5.60% | 3.33% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0432486247 | T -> C | LOC_Os04g54640.1 | upstream_gene_variant ; 693.0bp to feature; MODIFIER | silent_mutation | Average:61.421; most accessible tissue: Zhenshan97 flag leaf, score: 84.146 | N | N | N | N |
| vg0432486247 | T -> C | LOC_Os04g54640.2 | upstream_gene_variant ; 693.0bp to feature; MODIFIER | silent_mutation | Average:61.421; most accessible tissue: Zhenshan97 flag leaf, score: 84.146 | N | N | N | N |
| vg0432486247 | T -> C | LOC_Os04g54630.1 | downstream_gene_variant ; 4470.0bp to feature; MODIFIER | silent_mutation | Average:61.421; most accessible tissue: Zhenshan97 flag leaf, score: 84.146 | N | N | N | N |
| vg0432486247 | T -> C | LOC_Os04g54640-LOC_Os04g54650 | intergenic_region ; MODIFIER | silent_mutation | Average:61.421; most accessible tissue: Zhenshan97 flag leaf, score: 84.146 | N | N | N | N |
| vg0432486247 | T -> DEL | N | N | silent_mutation | Average:61.421; most accessible tissue: Zhenshan97 flag leaf, score: 84.146 | N | N | N | N |
| vg0432486247 | T -> TACAAGTTTTTTCTGCATACTTTGTCCTCA CTCATGTGCACTCGGGGAGAATTTCCCAAT CGGTCACTCATCCCCCCTTATAGACC | LOC_Os04g54640.1 | upstream_gene_variant ; 694.0bp to feature; MODIFIER | silent_mutation | Average:61.421; most accessible tissue: Zhenshan97 flag leaf, score: 84.146 | N | N | N | N |
| vg0432486247 | T -> TACAAGTTTTTTCTGCATACTTTGTCCTCA CTCATGTGCACTCGGGGAGAATTTCCCAAT CGGTCACTCATCCCCCCTTATAGACC | LOC_Os04g54640.2 | upstream_gene_variant ; 694.0bp to feature; MODIFIER | silent_mutation | Average:61.421; most accessible tissue: Zhenshan97 flag leaf, score: 84.146 | N | N | N | N |
| vg0432486247 | T -> TACAAGTTTTTTCTGCATACTTTGTCCTCA CTCATGTGCACTCGGGGAGAATTTCCCAAT CGGTCACTCATCCCCCCTTATAGACC | LOC_Os04g54630.1 | downstream_gene_variant ; 4471.0bp to feature; MODIFIER | silent_mutation | Average:61.421; most accessible tissue: Zhenshan97 flag leaf, score: 84.146 | N | N | N | N |
| vg0432486247 | T -> TACAAGTTTTTTCTGCATACTTTGTCCTCA CTCATGTGCACTCGGGGAGAATTTCCCAAT CGGTCACTCATCCCCCCTTATAGACC | LOC_Os04g54640-LOC_Os04g54650 | intergenic_region ; MODIFIER | silent_mutation | Average:61.421; most accessible tissue: Zhenshan97 flag leaf, score: 84.146 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0432486247 | 7.56E-07 | 3.16E-08 | mr1785 | 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 |
| vg0432486247 | NA | 5.24E-06 | mr1785 | 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 |
| vg0432486247 | 1.28E-09 | 1.89E-13 | mr1800 | 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 |
| vg0432486247 | 2.14E-07 | 4.83E-09 | mr1800 | 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 |
| vg0432486247 | NA | 1.65E-06 | mr1638_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 |
| vg0432486247 | NA | 1.15E-07 | mr1740_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 |
| vg0432486247 | 3.92E-06 | 5.44E-13 | mr1741_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 |
| vg0432486247 | NA | 2.09E-07 | mr1785_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 |
| vg0432486247 | 4.08E-12 | 1.38E-22 | mr1800_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 |
| vg0432486247 | 2.05E-10 | 1.68E-12 | mr1800_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 |