| Variant ID: vg0614715408 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 14715408 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 112. )
ACATGGAAAATAATTTATTCAAATACTAGATTATTTATCATGCCTAAATATAATTTTTCTAGAATTTTCCTCCTCTGTTTAGGCTTCCTAAAAATTCAAT[C/T]
TACCTTTCTAATAGCCCATATTTGTTTAATTTCTGTGAGCAGTCTATCCATTATTTTTTAGTGCAACCAAAGAAAATGGAATCTAGGTGTAATCGTTTAC
GTAAACGATTACACCTAGATTCCATTTTCTTTGGTTGCACTAAAAAATAATGGATAGACTGCTCACAGAAATTAAACAAATATGGGCTATTAGAAAGGTA[G/A]
ATTGAATTTTTAGGAAGCCTAAACAGAGGAGGAAAATTCTAGAAAAATTATATTTAGGCATGATAAATAATCTAGTATTTGAATAAATTATTTTCCATGT
| 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 | 40.00% | 31.30% | 5.37% | 23.36% | NA |
| All Indica | 2759 | 7.70% | 46.70% | 8.41% | 37.15% | NA |
| All Japonica | 1512 | 91.00% | 7.90% | 0.07% | 1.06% | NA |
| Aus | 269 | 71.40% | 16.40% | 4.09% | 8.18% | NA |
| Indica I | 595 | 15.50% | 12.80% | 12.44% | 59.33% | NA |
| Indica II | 465 | 6.50% | 27.30% | 9.46% | 56.77% | NA |
| Indica III | 913 | 1.80% | 84.00% | 3.72% | 10.51% | NA |
| Indica Intermediate | 786 | 9.50% | 40.60% | 10.18% | 39.69% | NA |
| Temperate Japonica | 767 | 96.10% | 2.50% | 0.00% | 1.43% | NA |
| Tropical Japonica | 504 | 82.50% | 16.90% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 92.50% | 6.20% | 0.41% | 0.83% | NA |
| VI/Aromatic | 96 | 63.50% | 4.20% | 8.33% | 23.96% | NA |
| Intermediate | 90 | 54.40% | 23.30% | 2.22% | 20.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0614715408 | C -> T | LOC_Os06g25150.1 | intron_variant ; MODIFIER | silent_mutation | Average:16.714; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
| vg0614715408 | C -> DEL | N | N | silent_mutation | Average:16.714; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0614715408 | NA | 1.76E-06 | mr1329_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 |
| vg0614715408 | NA | 5.86E-06 | mr1442_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 |
| vg0614715408 | NA | 4.52E-06 | mr1524_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 |
| vg0614715408 | NA | 3.55E-06 | mr1734_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 |
| vg0614715408 | 1.18E-06 | 1.18E-06 | mr1965_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 |