| Variant ID: vg1122274012 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 22274012 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GGTTCCCAGTAAAAAATATATTATGAGGTTTATATTGTAATTTTTTAATTTTATTTTCCCTTATATTTTGATCTGAACCGCAATTATTTATAACTATCTT[T/C]
GATTAAAAAATGAGGAGACATTTTGATGAGCTCTTAGTTCACAAATGACCAATATTATACTAGTTTATTGGCGATGCCATTATGCTCGTTATATCAATAT
ATATTGATATAACGAGCATAATGGCATCGCCAATAAACTAGTATAATATTGGTCATTTGTGAACTAAGAGCTCATCAAAATGTCTCCTCATTTTTTAATC[A/G]
AAGATAGTTATAAATAATTGCGGTTCAGATCAAAATATAAGGGAAAATAAAATTAAAAAATTACAATATAAACCTCATAATATATTTTTTACTGGGAACC
| 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 | 71.20% | 28.80% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 97.10% | 2.80% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 23.30% | 76.70% | 0.00% | 0.00% | NA |
| Aus | 269 | 72.50% | 27.50% | 0.00% | 0.00% | NA |
| Indica I | 595 | 96.50% | 3.50% | 0.00% | 0.00% | NA |
| Indica II | 465 | 97.40% | 2.60% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.30% | 0.50% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 94.90% | 5.00% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 20.70% | 79.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 17.50% | 82.50% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 43.60% | 56.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 75.00% | 25.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 73.30% | 26.70% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1122274012 | T -> C | LOC_Os11g37690.1 | upstream_gene_variant ; 2528.0bp to feature; MODIFIER | silent_mutation | Average:40.635; most accessible tissue: Zhenshan97 root, score: 87.992 | N | N | N | N |
| vg1122274012 | T -> C | LOC_Os11g37700.1 | intron_variant ; MODIFIER | silent_mutation | Average:40.635; most accessible tissue: Zhenshan97 root, score: 87.992 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1122274012 | 3.01E-06 | NA | mr1070 | 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 |
| vg1122274012 | NA | 3.92E-06 | mr1332 | 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 |
| vg1122274012 | NA | 8.40E-10 | mr1524 | 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 |
| vg1122274012 | NA | 2.63E-22 | mr1888 | 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 |