| Variant ID: vg1119375564 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 19375564 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 213. )
ACACTGTTGGTTGTGACTTGTATGTTAATAATCCGTCATATTGCTATCTGTATGAAGTAGATGGTAACAAATCCGAGTCATCGGCACCTGCATGCGCCGC[T/C]
GCTGCCGCCTGCACGTAGAGACACCCTGACGCCACCGCATGACGTATTCCCCTTTGTCAATGGTTGCCGAATCAATCCAGACCTGTCCTTGTCGATCCGC
GCGGATCGACAAGGACAGGTCTGGATTGATTCGGCAACCATTGACAAAGGGGAATACGTCATGCGGTGGCGTCAGGGTGTCTCTACGTGCAGGCGGCAGC[A/G]
GCGGCGCATGCAGGTGCCGATGACTCGGATTTGTTACCATCTACTTCATACAGATAGCAATATGACGGATTATTAACATACAAGTCACAACCAACAGTGT
| 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 | 64.20% | 32.40% | 0.30% | 3.15% | NA |
| All Indica | 2759 | 94.70% | 1.40% | 0.25% | 3.55% | NA |
| All Japonica | 1512 | 8.00% | 90.90% | 0.40% | 0.66% | NA |
| Aus | 269 | 79.20% | 5.20% | 0.37% | 15.24% | NA |
| Indica I | 595 | 96.50% | 1.50% | 0.34% | 1.68% | NA |
| Indica II | 465 | 91.60% | 0.20% | 0.43% | 7.74% | NA |
| Indica III | 913 | 97.70% | 1.00% | 0.00% | 1.31% | NA |
| Indica Intermediate | 786 | 91.90% | 2.70% | 0.38% | 5.09% | NA |
| Temperate Japonica | 767 | 4.20% | 93.70% | 0.78% | 1.30% | NA |
| Tropical Japonica | 504 | 11.10% | 88.90% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 13.70% | 86.30% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 29.20% | 70.80% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 63.30% | 36.70% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1119375564 | T -> DEL | LOC_Os11g32800.1 | N | frameshift_variant | Average:32.228; most accessible tissue: Zhenshan97 root, score: 72.188 | N | N | N | N |
| vg1119375564 | T -> C | LOC_Os11g32800.1 | missense_variant ; p.Gln115Arg; MODERATE | nonsynonymous_codon ; Q115R | Average:32.228; most accessible tissue: Zhenshan97 root, score: 72.188 | unknown | unknown | TOLERATED | 1.00 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1119375564 | 1.99E-06 | 1.99E-06 | mr1187_2 | 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 |
| vg1119375564 | NA | 5.16E-07 | mr1354_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 |