| Variant ID: vg1122472768 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 22472768 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TTAATGAAATGGGTAGATAAAATTTTAATGAAAGTTTTATGGACCTATTAAGATAGAACACACTTTACTTTTAAGTATTTGTATTTTTTTTAAAAAAAAA[T/C]
AATACAAGATGAATGATCAAAGTTTAAAGATAAATAGAATAAAGTCATAAGTAGTTGAACAGGGAGGGAGTAGATTATGGGTATGTGTGGCTGCACTTTT
AAAAGTGCAGCCACACATACCCATAATCTACTCCCTCCCTGTTCAACTACTTATGACTTTATTCTATTTATCTTTAAACTTTGATCATTCATCTTGTATT[A/G]
TTTTTTTTTAAAAAAAATACAAATACTTAAAAGTAAAGTGTGTTCTATCTTAATAGGTCCATAAAACTTTCATTAAAATTTTATCTACCCATTTCATTAA
| 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 | 93.10% | 6.50% | 0.40% | 0.00% | NA |
| All Indica | 2759 | 99.80% | 0.10% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 79.20% | 19.90% | 0.93% | 0.00% | NA |
| Aus | 269 | 98.90% | 0.00% | 1.12% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.80% | 0.10% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 87.60% | 11.00% | 1.43% | 0.00% | NA |
| Tropical Japonica | 504 | 61.30% | 38.50% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 89.60% | 9.50% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1122472768 | T -> C | LOC_Os11g37900.1 | upstream_gene_variant ; 1281.0bp to feature; MODIFIER | silent_mutation | Average:47.19; most accessible tissue: Callus, score: 79.73 | N | N | N | N |
| vg1122472768 | T -> C | LOC_Os11g37900-LOC_Os11g37910 | intergenic_region ; MODIFIER | silent_mutation | Average:47.19; most accessible tissue: Callus, score: 79.73 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1122472768 | 2.84E-06 | NA | mr1448 | 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 |
| vg1122472768 | NA | 1.14E-07 | mr1518 | 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 |
| vg1122472768 | NA | 4.72E-08 | mr1676 | 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 |
| vg1122472768 | 4.23E-06 | 4.23E-06 | mr1772 | Jap_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 |