| Variant ID: vg1108185945 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 8185945 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 82. )
GCACATACATGAATATTAGCACCAGTATCAACCCACCAATCAGGTGAATGAAAAACAGAGAGAACTGTAGGTAAAATTTTACCGTACCCCGATGTTCATC[C/T]
GCCCTCGCTAATGACCATGTTGGCAGACTTCCTGTCTTTGCGCTTAGGATAGACCTTGGCCCAATGCCTAGACTTGCCACATACAAAGCAGTCTCCCTTT
AAAGGGAGACTGCTTTGTATGTGGCAAGTCTAGGCATTGGGCCAAGGTCTATCCTAAGCGCAAAGACAGGAAGTCTGCCAACATGGTCATTAGCGAGGGC[G/A]
GATGAACATCGGGGTACGGTAAAATTTTACCTACAGTTCTCTCTGTTTTTCATTCACCTGATTGGTGGGTTGATACTGGTGCTAATATTCATGTATGTGC
| 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 | 55.30% | 39.60% | 4.99% | 0.08% | NA |
| All Indica | 2759 | 89.30% | 6.80% | 3.84% | 0.11% | NA |
| All Japonica | 1512 | 5.10% | 90.10% | 4.83% | 0.00% | NA |
| Aus | 269 | 8.90% | 72.50% | 18.59% | 0.00% | NA |
| Indica I | 595 | 89.20% | 9.70% | 1.01% | 0.00% | NA |
| Indica II | 465 | 95.90% | 2.60% | 1.29% | 0.22% | NA |
| Indica III | 913 | 90.80% | 3.60% | 5.59% | 0.00% | NA |
| Indica Intermediate | 786 | 83.60% | 10.70% | 5.47% | 0.25% | NA |
| Temperate Japonica | 767 | 1.80% | 98.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 6.90% | 81.20% | 11.90% | 0.00% | NA |
| Japonica Intermediate | 241 | 11.60% | 83.40% | 4.98% | 0.00% | NA |
| VI/Aromatic | 96 | 10.40% | 89.60% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 43.30% | 47.80% | 7.78% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1108185945 | C -> T | LOC_Os11g14560.1 | intron_variant ; MODIFIER | silent_mutation | Average:19.821; most accessible tissue: Callus, score: 30.038 | N | N | N | N |
| vg1108185945 | C -> DEL | N | N | silent_mutation | Average:19.821; most accessible tissue: Callus, score: 30.038 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1108185945 | 4.97E-06 | 4.97E-06 | mr1249 | 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 |
| vg1108185945 | NA | 4.75E-22 | mr1943 | 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 |
| vg1108185945 | NA | 3.82E-09 | mr1538_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 |
| vg1108185945 | NA | 1.37E-07 | mr1885_2 | 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 |