| Variant ID: vg1117717090 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 17717090 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 124. )
GTTCCACCGTCCTAATGGGGAATGGGTCACATGCTTCTGTTCATGGTGTTGGCACGGTAGATCTGAAGTTTACTTTGGGAAAGATCATGTAGGTGAAGAA[C/T]
GTGCAGCATGTCCCTTCTATCGACAGGAATCTTGTTAGTGGCTCCTGTCTGACTAGAGACGGATTTAAGTTGGTTTTTGAGTCTAATAAAGTAGTCGTGT
ACACGACTACTTTATTAGACTCAAAAACCAACTTAAATCCGTCTCTAGTCAGACAGGAGCCACTAACAAGATTCCTGTCGATAGAAGGGACATGCTGCAC[G/A]
TTCTTCACCTACATGATCTTTCCCAAAGTAAACTTCAGATCTACCGTGCCAACACCATGAACAGAAGCATGTGACCCATTCCCCATTAGGACGGTGGAAC
| 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 | 26.90% | 10.10% | 50.02% | 12.99% | NA |
| All Indica | 2759 | 12.60% | 5.40% | 60.86% | 21.09% | NA |
| All Japonica | 1512 | 52.50% | 21.30% | 24.93% | 1.26% | NA |
| Aus | 269 | 17.80% | 0.00% | 79.93% | 2.23% | NA |
| Indica I | 595 | 8.60% | 14.30% | 34.29% | 42.86% | NA |
| Indica II | 465 | 25.20% | 1.30% | 58.28% | 15.27% | NA |
| Indica III | 913 | 8.40% | 2.50% | 78.64% | 10.41% | NA |
| Indica Intermediate | 786 | 13.10% | 4.60% | 61.83% | 20.48% | NA |
| Temperate Japonica | 767 | 58.50% | 39.40% | 1.43% | 0.65% | NA |
| Tropical Japonica | 504 | 29.40% | 3.20% | 65.08% | 2.38% | NA |
| Japonica Intermediate | 241 | 81.70% | 1.70% | 15.77% | 0.83% | NA |
| VI/Aromatic | 96 | 50.00% | 2.10% | 47.92% | 0.00% | NA |
| Intermediate | 90 | 34.40% | 5.60% | 52.22% | 7.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1117717090 | C -> T | LOC_Os11g30484.1 | upstream_gene_variant ; 4990.0bp to feature; MODIFIER | silent_mutation | Average:18.034; most accessible tissue: Minghui63 young leaf, score: 31.294 | N | N | N | N |
| vg1117717090 | C -> T | LOC_Os11g30470.1 | intron_variant ; MODIFIER | silent_mutation | Average:18.034; most accessible tissue: Minghui63 young leaf, score: 31.294 | N | N | N | N |
| vg1117717090 | C -> DEL | N | N | silent_mutation | Average:18.034; most accessible tissue: Minghui63 young leaf, score: 31.294 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1117717090 | NA | 9.61E-13 | Heading_date | All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg1117717090 | NA | 2.67E-06 | mr1002 | 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 |
| vg1117717090 | NA | 8.82E-06 | mr1354 | Jap_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 |
| vg1117717090 | 2.06E-06 | 1.83E-10 | mr1002_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 |
| vg1117717090 | NA | 1.72E-06 | mr1354_2 | Jap_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 |
| vg1117717090 | NA | 6.55E-06 | mr1902_2 | Jap_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 |