| Variant ID: vg0409861333 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9861333 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CACACGTGGGTGCGATCTTTTTGACCGGAATGAAAAAGTTCAAAAAGCACTAAAACAATATTTTCGCACATATTATAGTGTATTGGGTGCAATCATTGAA[C/A]
AAAGTCACTTCCTGATTCGCGCAGCCATCTTTTGTCAATTAATGCCAATATTAGGATACACATGTGGGTGTGATGTTTTTGACCGGAATGAAAAAGATCA
TGATCTTTTTCATTCCGGTCAAAAACATCACACCCACATGTGTATCCTAATATTGGCATTAATTGACAAAAGATGGCTGCGCGAATCAGGAAGTGACTTT[G/T]
TTCAATGATTGCACCCAATACACTATAATATGTGCGAAAATATTGTTTTAGTGCTTTTTGAACTTTTTCATTCCGGTCAAAAAGATCGCACCCACGTGTG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 37.20% | 0.20% | 39.65% | 23.00% | NA |
| All Indica | 2759 | 28.30% | 0.30% | 54.22% | 17.18% | NA |
| All Japonica | 1512 | 61.20% | 0.00% | 4.96% | 33.80% | NA |
| Aus | 269 | 5.90% | 0.40% | 88.85% | 4.83% | NA |
| Indica I | 595 | 39.70% | 0.00% | 42.18% | 18.15% | NA |
| Indica II | 465 | 26.00% | 0.20% | 58.49% | 15.27% | NA |
| Indica III | 913 | 27.60% | 0.30% | 55.64% | 16.43% | NA |
| Indica Intermediate | 786 | 22.00% | 0.40% | 59.16% | 18.45% | NA |
| Temperate Japonica | 767 | 96.00% | 0.00% | 0.52% | 3.52% | NA |
| Tropical Japonica | 504 | 4.60% | 0.00% | 11.51% | 83.93% | NA |
| Japonica Intermediate | 241 | 69.30% | 0.00% | 5.39% | 25.31% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 29.17% | 68.75% | NA |
| Intermediate | 90 | 33.30% | 1.10% | 40.00% | 25.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409861333 | C -> DEL | N | N | silent_mutation | Average:23.621; most accessible tissue: Minghui63 panicle, score: 56.842 | N | N | N | N |
| vg0409861333 | C -> A | LOC_Os04g17930.1 | upstream_gene_variant ; 4118.0bp to feature; MODIFIER | silent_mutation | Average:23.621; most accessible tissue: Minghui63 panicle, score: 56.842 | N | N | N | N |
| vg0409861333 | C -> A | LOC_Os04g17940.1 | downstream_gene_variant ; 1067.0bp to feature; MODIFIER | silent_mutation | Average:23.621; most accessible tissue: Minghui63 panicle, score: 56.842 | N | N | N | N |
| vg0409861333 | C -> A | LOC_Os04g17930-LOC_Os04g17940 | intergenic_region ; MODIFIER | silent_mutation | Average:23.621; most accessible tissue: Minghui63 panicle, score: 56.842 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0409861333 | NA | 6.13E-06 | mr1111 | 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 |
| vg0409861333 | NA | 7.27E-07 | mr1690 | 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 |
| vg0409861333 | NA | 4.70E-42 | mr1719 | 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 |
| vg0409861333 | NA | 1.92E-70 | mr1019_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 |