| Variant ID: vg0408380913 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 8380913 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.06, others allele: 0.00, population size: 104. )
TCCGAACCTTCCTCAACGAAAGCGCTCTCCTCCGGAACGTCGGAAACTAAAGCAAAAGAACAAAATCAACAAAACAGTACAAAAACAAGCATAAACAGTA[C/T]
ATGTGGATATTTTTAGTATGTAGATCTTGATTTTAGAAAAATTTAGCAACTTGAACCACTCGAATCGGAGTTACGATGATTTAGTTACGAATTTCCAAAG
CTTTGGAAATTCGTAACTAAATCATCGTAACTCCGATTCGAGTGGTTCAAGTTGCTAAATTTTTCTAAAATCAAGATCTACATACTAAAAATATCCACAT[G/A]
TACTGTTTATGCTTGTTTTTGTACTGTTTTGTTGATTTTGTTCTTTTGCTTTAGTTTCCGACGTTCCGGAGGAGAGCGCTTTCGTTGAGGAAGGTTCGGA
| 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 | 33.60% | 3.80% | 35.93% | 26.75% | NA |
| All Indica | 2759 | 18.60% | 4.50% | 43.57% | 33.38% | NA |
| All Japonica | 1512 | 66.20% | 2.00% | 16.34% | 15.48% | NA |
| Aus | 269 | 14.90% | 5.20% | 53.90% | 26.02% | NA |
| Indica I | 595 | 28.90% | 0.70% | 36.47% | 33.95% | NA |
| Indica II | 465 | 18.70% | 2.40% | 43.01% | 35.91% | NA |
| Indica III | 913 | 11.30% | 9.00% | 48.30% | 31.43% | NA |
| Indica Intermediate | 786 | 19.10% | 3.40% | 43.77% | 33.72% | NA |
| Temperate Japonica | 767 | 96.20% | 0.00% | 0.52% | 3.26% | NA |
| Tropical Japonica | 504 | 17.70% | 5.80% | 41.47% | 35.12% | NA |
| Japonica Intermediate | 241 | 72.20% | 0.40% | 14.11% | 13.28% | NA |
| VI/Aromatic | 96 | 3.10% | 7.30% | 71.88% | 17.71% | NA |
| Intermediate | 90 | 33.30% | 3.30% | 38.89% | 24.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0408380913 | C -> DEL | N | N | silent_mutation | Average:8.47; most accessible tissue: Callus, score: 16.142 | N | N | N | N |
| vg0408380913 | C -> T | LOC_Os04g14890.1 | upstream_gene_variant ; 54.0bp to feature; MODIFIER | silent_mutation | Average:8.47; most accessible tissue: Callus, score: 16.142 | N | N | N | N |
| vg0408380913 | C -> T | LOC_Os04g14900.1 | downstream_gene_variant ; 2218.0bp to feature; MODIFIER | silent_mutation | Average:8.47; most accessible tissue: Callus, score: 16.142 | N | N | N | N |
| vg0408380913 | C -> T | LOC_Os04g14890-LOC_Os04g14900 | intergenic_region ; MODIFIER | silent_mutation | Average:8.47; most accessible tissue: Callus, score: 16.142 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0408380913 | 1.90E-07 | NA | mr1016 | 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 |
| vg0408380913 | 6.55E-06 | NA | mr1017 | 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 |
| vg0408380913 | 7.53E-07 | NA | mr1055 | 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 |
| vg0408380913 | 2.58E-06 | NA | mr1142 | 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 |
| vg0408380913 | 8.85E-06 | 1.32E-06 | mr1750 | 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 |