| Variant ID: vg0719611742 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 19611742 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.71, T: 0.29, others allele: 0.00, population size: 99. )
GTATTTTAAAAATAACATAATTATCGTTTAGTTTTTTTTTACTTTCTAGAAGTTCCGCCAAAACGTCAACGACTTTGTCACTATACTTCTCTACGGCTCG[C/T]
CCGCTGTCGCATTTTTTTTATTGTCATTGAGATTTAAAAATCAAACATGATTATCATTGAGATTTATTTTTTTACTTTTTAGAAGCCTGAACGTTTAAAA
TTTTAAACGTTCAGGCTTCTAAAAAGTAAAAAAATAAATCTCAATGATAATCATGTTTGATTTTTAAATCTCAATGACAATAAAAAAAATGCGACAGCGG[G/A]
CGAGCCGTAGAGAAGTATAGTGACAAAGTCGTTGACGTTTTGGCGGAACTTCTAGAAAGTAAAAAAAAACTAAACGATAATTATGTTATTTTTAAAATAC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 75.20% | 23.20% | 1.14% | 0.49% | NA |
| All Indica | 2759 | 86.90% | 10.70% | 1.59% | 0.80% | NA |
| All Japonica | 1512 | 48.50% | 51.30% | 0.26% | 0.00% | NA |
| Aus | 269 | 97.40% | 1.90% | 0.74% | 0.00% | NA |
| Indica I | 595 | 88.70% | 6.60% | 3.36% | 1.34% | NA |
| Indica II | 465 | 82.60% | 15.50% | 1.29% | 0.65% | NA |
| Indica III | 913 | 85.00% | 13.60% | 0.77% | 0.66% | NA |
| Indica Intermediate | 786 | 90.30% | 7.60% | 1.40% | 0.64% | NA |
| Temperate Japonica | 767 | 46.30% | 53.30% | 0.39% | 0.00% | NA |
| Tropical Japonica | 504 | 56.00% | 43.80% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 39.80% | 60.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 1.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 74.40% | 21.10% | 3.33% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0719611742 | C -> DEL | N | N | silent_mutation | Average:34.112; most accessible tissue: Minghui63 panicle, score: 62.157 | N | N | N | N |
| vg0719611742 | C -> T | LOC_Os07g32774.1 | upstream_gene_variant ; 2697.0bp to feature; MODIFIER | silent_mutation | Average:34.112; most accessible tissue: Minghui63 panicle, score: 62.157 | N | N | N | N |
| vg0719611742 | C -> T | LOC_Os07g32790.1 | downstream_gene_variant ; 2499.0bp to feature; MODIFIER | silent_mutation | Average:34.112; most accessible tissue: Minghui63 panicle, score: 62.157 | N | N | N | N |
| vg0719611742 | C -> T | LOC_Os07g32774-LOC_Os07g32790 | intergenic_region ; MODIFIER | silent_mutation | Average:34.112; most accessible tissue: Minghui63 panicle, score: 62.157 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0719611742 | 8.03E-06 | NA | mr1086 | 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 |
| vg0719611742 | 2.59E-06 | 2.59E-06 | mr1193 | 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 |
| vg0719611742 | NA | 1.02E-09 | mr1709_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 |
| vg0719611742 | NA | 2.00E-08 | mr1821_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 |