| Variant ID: vg0819107411 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr08 | Position: 19107411 |
| Reference Allele: T | Alternative Allele: C,TC |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 53. )
AGAGGGCAATGAAGACAGGAAGACTCAATGGTGTCCTTCTGGTATCTTTATAAAGAATCAGAAGAGAAGGGTTCAAAGATTGAGGAACAGGGAGCACTTT[T/C,TC]
AGGAGGTCGAACAGGAAATCAATCATCGGCTAAAGAAAATGAAGCCGAAGCAGGAGTGGCGAGTTAAGAATCAAGCTCCTATAGCCGATGAGGCCGCAGC
GCTGCGGCCTCATCGGCTATAGGAGCTTGATTCTTAACTCGCCACTCCTGCTTCGGCTTCATTTTCTTTAGCCGATGATTGATTTCCTGTTCGACCTCCT[A/G,GA]
AAAGTGCTCCCTGTTCCTCAATCTTTGAACCCTTCTCTTCTGATTCTTTATAAAGATACCAGAAGGACACCATTGAGTCTTCCTGTCTTCATTGCCCTCT
| 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 | 73.30% | 8.30% | 14.26% | 3.60% | TC: 0.53% |
| All Indica | 2759 | 66.00% | 10.80% | 22.04% | 0.29% | TC: 0.91% |
| All Japonica | 1512 | 87.60% | 0.10% | 1.72% | 10.58% | NA |
| Aus | 269 | 54.60% | 33.50% | 11.90% | 0.00% | NA |
| Indica I | 595 | 74.50% | 3.90% | 20.34% | 0.17% | TC: 1.18% |
| Indica II | 465 | 75.90% | 3.70% | 18.28% | 0.22% | TC: 1.94% |
| Indica III | 913 | 58.40% | 18.80% | 22.12% | 0.11% | TC: 0.55% |
| Indica Intermediate | 786 | 62.60% | 10.80% | 25.45% | 0.64% | TC: 0.51% |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 68.80% | 0.40% | 3.97% | 26.79% | NA |
| Japonica Intermediate | 241 | 87.60% | 0.00% | 2.07% | 10.37% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 1.04% | 1.04% | NA |
| Intermediate | 90 | 85.60% | 5.60% | 7.78% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0819107411 | T -> C | LOC_Os08g30950.1 | upstream_gene_variant ; 39.0bp to feature; MODIFIER | silent_mutation | Average:12.839; most accessible tissue: Zhenshan97 root, score: 22.162 | N | N | N | N |
| vg0819107411 | T -> C | LOC_Os08g30940.1 | downstream_gene_variant ; 382.0bp to feature; MODIFIER | silent_mutation | Average:12.839; most accessible tissue: Zhenshan97 root, score: 22.162 | N | N | N | N |
| vg0819107411 | T -> C | LOC_Os08g30940-LOC_Os08g30950 | intergenic_region ; MODIFIER | silent_mutation | Average:12.839; most accessible tissue: Zhenshan97 root, score: 22.162 | N | N | N | N |
| vg0819107411 | T -> DEL | N | N | silent_mutation | Average:12.839; most accessible tissue: Zhenshan97 root, score: 22.162 | N | N | N | N |
| vg0819107411 | T -> TC | LOC_Os08g30950.1 | upstream_gene_variant ; 38.0bp to feature; MODIFIER | silent_mutation | Average:12.839; most accessible tissue: Zhenshan97 root, score: 22.162 | N | N | N | N |
| vg0819107411 | T -> TC | LOC_Os08g30940.1 | downstream_gene_variant ; 383.0bp to feature; MODIFIER | silent_mutation | Average:12.839; most accessible tissue: Zhenshan97 root, score: 22.162 | N | N | N | N |
| vg0819107411 | T -> TC | LOC_Os08g30940-LOC_Os08g30950 | intergenic_region ; MODIFIER | silent_mutation | Average:12.839; most accessible tissue: Zhenshan97 root, score: 22.162 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0819107411 | NA | 1.66E-06 | mr1028 | 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 |
| vg0819107411 | 1.02E-06 | NA | mr1276 | 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 |
| vg0819107411 | 3.87E-06 | 3.87E-06 | mr1276 | 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 |
| vg0819107411 | 2.43E-06 | 8.92E-07 | mr1755 | 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 |
| vg0819107411 | NA | 3.76E-07 | mr1835 | 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 |