| Variant ID: vg0817973700 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17973700 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 109. )
TACGGATCAATTGCTACGAGGCGCACCAATCGAAAAGGCGGAAGTGAAATACATGTACGAACTCGGTAAACCGCTTGTCAAGCATGAGCAGCTGCAGTCC[C/T]
TACCTACAGAAATGTACAAGTTCCATCAACTGTACATGGAGATGAGCGCCACCGGTAGAGAGATGATCGGAGCGAGGATCAGGGACACGGACTTCTTGCA
TGCAAGAAGTCCGTGTCCCTGATCCTCGCTCCGATCATCTCTCTACCGGTGGCGCTCATCTCCATGTACAGTTGATGGAACTTGTACATTTCTGTAGGTA[G/A]
GGACTGCAGCTGCTCATGCTTGACAAGCGGTTTACCGAGTTCGTACATGTATTTCACTTCCGCCTTTTCGATTGGTGCGCCTCGTAGCAATTGATCCGTA
| 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 | 77.10% | 8.80% | 6.62% | 7.55% | NA |
| All Indica | 2759 | 76.20% | 8.40% | 4.71% | 10.69% | NA |
| All Japonica | 1512 | 87.80% | 11.60% | 0.33% | 0.26% | NA |
| Aus | 269 | 15.60% | 1.10% | 63.20% | 20.07% | NA |
| Indica I | 595 | 66.60% | 27.60% | 1.34% | 4.54% | NA |
| Indica II | 465 | 93.80% | 2.20% | 1.29% | 2.80% | NA |
| Indica III | 913 | 78.90% | 0.50% | 7.12% | 13.47% | NA |
| Indica Intermediate | 786 | 70.10% | 6.60% | 6.49% | 16.79% | NA |
| Temperate Japonica | 767 | 98.70% | 1.00% | 0.00% | 0.26% | NA |
| Tropical Japonica | 504 | 72.80% | 25.80% | 0.99% | 0.40% | NA |
| Japonica Intermediate | 241 | 84.60% | 15.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 2.08% | 1.04% | NA |
| Intermediate | 90 | 84.40% | 5.60% | 6.67% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817973700 | C -> T | LOC_Os08g29290.1 | synonymous_variant ; p.Leu1156Leu; LOW | synonymous_codon | Average:22.711; most accessible tissue: Callus, score: 40.5 | N | N | N | N |
| vg0817973700 | C -> DEL | LOC_Os08g29290.1 | N | frameshift_variant | Average:22.711; most accessible tissue: Callus, score: 40.5 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0817973700 | NA | 1.87E-11 | mr1410 | 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 |
| vg0817973700 | NA | 6.01E-07 | mr1739 | 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 |
| vg0817973700 | NA | 1.29E-06 | mr1860_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 |
| vg0817973700 | 3.97E-07 | 5.62E-12 | mr1993_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 |