| Variant ID: vg0907521059 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 7521059 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 107. )
CCGACCCGAGTGTAAGATTCCGTTATTATGCCCTCCGCAGAGGCCGGCTGCGGTGTGCATCGGCCCCAACCACCACAATCCCTTCTACCACCTGATGGAG[C/G]
AGGAGAAGAAGGTGATGCTCTACGGCATTCTGATCCTGGTGGACGAGCAGCACAAGGCTGCCGTGCTGAGGAGATTAGTGGATGCGGTCACTGCCCTCGA
TCGAGGGCAGTGACCGCATCCACTAATCTCCTCAGCACGGCAGCCTTGTGCTGCTCGTCCACCAGGATCAGAATGCCGTAGAGCATCACCTTCTTCTCCT[G/C]
CTCCATCAGGTGGTAGAAGGGATTGTGGTGGTTGGGGCCGATGCACACCGCAGCCGGCCTCTGCGGAGGGCATAATAACGGAATCTTACACTCGGGTCGG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 66.70% | 29.30% | 1.71% | 2.22% | NA |
| All Indica | 2759 | 58.00% | 36.40% | 2.61% | 3.01% | NA |
| All Japonica | 1512 | 79.60% | 19.40% | 0.40% | 0.60% | NA |
| Aus | 269 | 66.90% | 28.30% | 0.74% | 4.09% | NA |
| Indica I | 595 | 36.80% | 55.80% | 5.38% | 2.02% | NA |
| Indica II | 465 | 83.00% | 12.70% | 1.29% | 3.01% | NA |
| Indica III | 913 | 59.90% | 35.00% | 0.77% | 4.27% | NA |
| Indica Intermediate | 786 | 56.90% | 37.40% | 3.44% | 2.29% | NA |
| Temperate Japonica | 767 | 92.30% | 7.30% | 0.26% | 0.13% | NA |
| Tropical Japonica | 504 | 76.00% | 23.40% | 0.40% | 0.20% | NA |
| Japonica Intermediate | 241 | 46.90% | 49.40% | 0.83% | 2.90% | NA |
| VI/Aromatic | 96 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 85.60% | 11.10% | 1.11% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0907521059 | C -> G | LOC_Os09g13040.1 | missense_variant ; p.Gln102Glu; MODERATE | nonsynonymous_codon ; Q102E | Average:68.197; most accessible tissue: Zhenshan97 young leaf, score: 91.899 | unknown | unknown | TOLERATED | 1.00 |
| vg0907521059 | C -> DEL | LOC_Os09g13040.1 | N | frameshift_variant | Average:68.197; most accessible tissue: Zhenshan97 young leaf, score: 91.899 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0907521059 | NA | 8.52E-06 | mr1159_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 |
| vg0907521059 | NA | 2.10E-06 | mr1332_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 |
| vg0907521059 | NA | 9.48E-09 | mr1371_2 | 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 |
| vg0907521059 | NA | 4.90E-06 | mr1371_2 | 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 |
| vg0907521059 | NA | 1.95E-06 | mr1417_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 |
| vg0907521059 | NA | 3.38E-06 | mr1445_2 | 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 |
| vg0907521059 | NA | 1.67E-06 | mr1647_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 |
| vg0907521059 | NA | 8.25E-07 | mr1655_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 |
| vg0907521059 | NA | 5.70E-06 | mr1895_2 | 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 |
| vg0907521059 | NA | 2.38E-07 | mr1977_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 |