| Variant ID: vg1117245312 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 17245312 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 66. )
GCACTGCCACTGCTCCCTTCCCCACCCCCAACGCCCTGGTGTGTCTCCATCGCTGGATCCGCCGTCCCCGCGCATCGCCTTCCCTGGATCCACCACACCC[G/A]
CACATCACTATCTCTAGATCCCACCACCCCCCCACTGTACTCTGCCAAACGCGTCGCAGCTGCTCCCTTCCCCACCACCGCCGCCCTCGTCGCCGCTCCC
GGGAGCGGCGACGAGGGCGGCGGTGGTGGGGAAGGGAGCAGCTGCGACGCGTTTGGCAGAGTACAGTGGGGGGGTGGTGGGATCTAGAGATAGTGATGTG[C/T]
GGGTGTGGTGGATCCAGGGAAGGCGATGCGCGGGGACGGCGGATCCAGCGATGGAGACACACCAGGGCGTTGGGGGTGGGGAAGGGAGCAGTGGCAGTGC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 27.90% | 27.10% | 0.99% | 44.03% | NA |
| All Indica | 2759 | 37.90% | 14.00% | 0.87% | 47.30% | NA |
| All Japonica | 1512 | 4.40% | 53.70% | 1.06% | 40.87% | NA |
| Aus | 269 | 67.70% | 19.00% | 0.74% | 12.64% | NA |
| Indica I | 595 | 17.00% | 21.30% | 1.01% | 60.67% | NA |
| Indica II | 465 | 33.30% | 18.90% | 1.29% | 46.45% | NA |
| Indica III | 913 | 53.60% | 5.80% | 0.22% | 40.42% | NA |
| Indica Intermediate | 786 | 38.20% | 14.90% | 1.27% | 45.67% | NA |
| Temperate Japonica | 767 | 0.00% | 85.50% | 0.52% | 13.95% | NA |
| Tropical Japonica | 504 | 12.30% | 18.50% | 1.79% | 67.46% | NA |
| Japonica Intermediate | 241 | 1.70% | 26.10% | 1.24% | 70.95% | NA |
| VI/Aromatic | 96 | 5.20% | 0.00% | 3.12% | 91.67% | NA |
| Intermediate | 90 | 22.20% | 35.60% | 2.22% | 40.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1117245312 | G -> A | LOC_Os11g29730.1 | intron_variant ; MODIFIER | silent_mutation | Average:51.38; most accessible tissue: Zhenshan97 young leaf, score: 97.404 | N | N | N | N |
| vg1117245312 | G -> DEL | N | N | silent_mutation | Average:51.38; most accessible tissue: Zhenshan97 young leaf, score: 97.404 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1117245312 | NA | 1.33E-06 | mr1090 | 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 |
| vg1117245312 | NA | 2.79E-07 | mr1090_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 |
| vg1117245312 | NA | 1.62E-06 | mr1121_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 |
| vg1117245312 | NA | 1.53E-06 | mr1125_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 |
| vg1117245312 | NA | 3.53E-06 | mr1181_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 |
| vg1117245312 | 2.45E-06 | NA | mr1477_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 |