| Variant ID: vg0208434103 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 8434103 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 99. )
ATATACATACGACATCACCGTTGCCCTTTTGCTCGAGAAACCATTTTGTCAAGAAAGTAAACTGCAATTGGAAAACGTAGGATTACGTCAAGGTCAACTA[C/T]
TTGGTCCTTTTATCTGGGCAATATGCCACGACATGATCGGATTTTAAATCTGGACAGAGGTTAGAATCTTAACTGCCAAATAGGAATGCTCTATTGGTTC
GAACCAATAGAGCATTCCTATTTGGCAGTTAAGATTCTAACCTCTGTCCAGATTTAAAATCCGATCATGTCGTGGCATATTGCCCAGATAAAAGGACCAA[G/A]
TAGTTGACCTTGACGTAATCCTACGTTTTCCAATTGCAGTTTACTTTCTTGACAAAATGGTTTCTCGAGCAAAAGGGCAACGGTGATGTCGTATGTATAT
| 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 | 87.60% | 11.50% | 0.87% | 0.00% | NA |
| All Indica | 2759 | 83.80% | 15.40% | 0.80% | 0.00% | NA |
| All Japonica | 1512 | 91.70% | 7.20% | 1.12% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 62.90% | 35.00% | 2.18% | 0.00% | NA |
| Indica II | 465 | 94.80% | 4.70% | 0.43% | 0.00% | NA |
| Indica III | 913 | 90.50% | 9.50% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 85.50% | 13.60% | 0.89% | 0.00% | NA |
| Temperate Japonica | 767 | 99.00% | 0.40% | 0.65% | 0.00% | NA |
| Tropical Japonica | 504 | 78.00% | 19.80% | 2.18% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.10% | 2.50% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 94.80% | 4.20% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 6.70% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0208434103 | C -> T | LOC_Os02g15130.1 | downstream_gene_variant ; 4829.0bp to feature; MODIFIER | silent_mutation | Average:40.343; most accessible tissue: Zhenshan97 young leaf, score: 64.205 | N | N | N | N |
| vg0208434103 | C -> T | LOC_Os02g15140.1 | intron_variant ; MODIFIER | silent_mutation | Average:40.343; most accessible tissue: Zhenshan97 young leaf, score: 64.205 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0208434103 | NA | 2.62E-06 | mr1336 | 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 |
| vg0208434103 | NA | 3.93E-06 | mr1324_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 |
| vg0208434103 | 4.80E-06 | 4.79E-06 | mr1325_2 | 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 |
| vg0208434103 | NA | 1.07E-07 | mr1623_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 |