| Variant ID: vg1121617785 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 21617785 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.70, T: 0.30, others allele: 0.00, population size: 50. )
CACATCTATGGCCAGGGTCTGTAGAGAACTTCGAGTGGTCCGCGGAGATCCCGAGGAGTCGGCGGCCGGATACATCTCATGGCTGAACGGGGCCTGTGCC[C/T]
AACTCAATGGCATCGGCAAGCGTATCGACGAGGCCTTGAAGCAGGAGTGTCGTCGATCGAGCCGGTATGCCGGAGGGCACGTGTTGGCTTGCCCGCGAGA
TCTCGCGGGCAAGCCAACACGTGCCCTCCGGCATACCGGCTCGATCGACGACACTCCTGCTTCAAGGCCTCGTCGATACGCTTGCCGATGCCATTGAGTT[G/A]
GGCACAGGCCCCGTTCAGCCATGAGATGTATCCGGCCGCCGACTCCTCGGGATCTCCGCGGACCACTCGAAGTTCTCTACAGACCCTGGCCATAGATGTG
| 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 | 31.90% | 20.30% | 30.62% | 17.20% | NA |
| All Indica | 2759 | 12.00% | 32.60% | 41.83% | 13.56% | NA |
| All Japonica | 1512 | 72.60% | 2.50% | 5.82% | 19.11% | NA |
| Aus | 269 | 13.40% | 2.20% | 53.53% | 30.86% | NA |
| Indica I | 595 | 20.20% | 13.10% | 38.82% | 27.90% | NA |
| Indica II | 465 | 9.20% | 53.10% | 28.60% | 9.03% | NA |
| Indica III | 913 | 5.30% | 34.40% | 51.59% | 8.76% | NA |
| Indica Intermediate | 786 | 15.40% | 33.10% | 40.59% | 10.94% | NA |
| Temperate Japonica | 767 | 82.30% | 0.80% | 2.22% | 14.73% | NA |
| Tropical Japonica | 504 | 58.90% | 5.60% | 10.71% | 24.80% | NA |
| Japonica Intermediate | 241 | 70.10% | 1.70% | 7.05% | 21.16% | NA |
| VI/Aromatic | 96 | 7.30% | 4.20% | 41.67% | 46.88% | NA |
| Intermediate | 90 | 37.80% | 14.40% | 23.33% | 24.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1121617785 | C -> T | LOC_Os11g36630.1 | stop_gained ; p.Gln645*; HIGH | stop_gained | Average:10.962; most accessible tissue: Callus, score: 38.666 | N | N | N | N |
| vg1121617785 | C -> DEL | LOC_Os11g36630.1 | N | frameshift_variant | Average:10.962; most accessible tissue: Callus, score: 38.666 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1121617785 | 5.87E-07 | 5.25E-09 | mr1053 | 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 |
| vg1121617785 | 3.32E-07 | 2.88E-07 | mr1053 | 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 |
| vg1121617785 | 2.26E-06 | 1.00E-06 | mr1147 | 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 |