| Variant ID: vg0618478943 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 18478943 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 84. )
AAGCTATACTTCAAATCAAGCAGTTACCCATTCCCGCTTGTGGTAAGCGCGGTAAATCTTCCACTGCATCCCGCGAACCAGTCATTAATTGCCATGGGTG[C/T]
GACTAGTAAAACCATGCATCCACAAGGCACCACTCAGTCGCATTTTAATTGGATAATTACGACCAATGAAACATGGCCACTTAATTTTAGTGGTAATTAA
TTAATTACCACTAAAATTAAGTGGCCATGTTTCATTGGTCGTAATTATCCAATTAAAATGCGACTGAGTGGTGCCTTGTGGATGCATGGTTTTACTAGTC[G/A]
CACCCATGGCAATTAATGACTGGTTCGCGGGATGCAGTGGAAGATTTACCGCGCTTACCACAAGCGGGAATGGGTAACTGCTTGATTTGAAGTATAGCTT
| 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 | 23.50% | 7.00% | 10.62% | 58.82% | NA |
| All Indica | 2759 | 6.00% | 1.30% | 8.77% | 83.91% | NA |
| All Japonica | 1512 | 60.80% | 18.80% | 12.63% | 7.67% | NA |
| Aus | 269 | 0.40% | 0.00% | 4.83% | 94.80% | NA |
| Indica I | 595 | 7.60% | 0.50% | 20.34% | 71.60% | NA |
| Indica II | 465 | 4.10% | 2.60% | 8.60% | 84.73% | NA |
| Indica III | 913 | 2.70% | 0.90% | 1.31% | 95.07% | NA |
| Indica Intermediate | 786 | 9.70% | 1.80% | 8.78% | 79.77% | NA |
| Temperate Japonica | 767 | 75.60% | 0.50% | 18.38% | 5.48% | NA |
| Tropical Japonica | 504 | 32.90% | 52.40% | 3.17% | 11.51% | NA |
| Japonica Intermediate | 241 | 72.20% | 7.10% | 14.11% | 6.64% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 45.83% | 52.08% | NA |
| Intermediate | 90 | 25.60% | 12.20% | 13.33% | 48.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0618478943 | C -> T | LOC_Os06g31810.1 | upstream_gene_variant ; 4724.0bp to feature; MODIFIER | silent_mutation | Average:16.561; most accessible tissue: Minghui63 panicle, score: 42.799 | N | N | N | N |
| vg0618478943 | C -> T | LOC_Os06g31820.1 | upstream_gene_variant ; 6.0bp to feature; MODIFIER | silent_mutation | Average:16.561; most accessible tissue: Minghui63 panicle, score: 42.799 | N | N | N | N |
| vg0618478943 | C -> T | LOC_Os06g31820-LOC_Os06g31830 | intergenic_region ; MODIFIER | silent_mutation | Average:16.561; most accessible tissue: Minghui63 panicle, score: 42.799 | N | N | N | N |
| vg0618478943 | C -> DEL | N | N | silent_mutation | Average:16.561; most accessible tissue: Minghui63 panicle, score: 42.799 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0618478943 | NA | 4.21E-06 | mr1852 | 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 |
| vg0618478943 | 1.27E-06 | NA | mr1925 | 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 |
| vg0618478943 | NA | 2.29E-09 | mr1993 | 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 |
| vg0618478943 | NA | 2.43E-07 | mr1408_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 |
| vg0618478943 | 3.65E-06 | 4.10E-14 | mr1993_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 |