| Variant ID: vg1218655720 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18655720 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.69, A: 0.31, others allele: 0.00, population size: 74. )
ACAAAGATGATGCACCGGTGGATGAGAACAAAAAGATTCCTAGGATGGTGATGTGGTACGTGCCAGTTAAAGATCGCCTGAAGCGGCTATATTCCAACCG[A/T]
GACGACGCCAAGTTGATGAGATGGCACCAGGAGGGTAGGAAAAATGACGGTAAGATCCGACACCCCGCCGATGCTCGACAGTGGAAAAACTTTGATGCAC
GTGCATCAAAGTTTTTCCACTGTCGAGCATCGGCGGGGTGTCGGATCTTACCGTCATTTTTCCTACCCTCCTGGTGCCATCTCATCAACTTGGCGTCGTC[T/A]
CGGTTGGAATATAGCCGCTTCAGGCGATCTTTAACTGGCACGTACCACATCACCATCCTAGGAATCTTTTTGTTCTCATCCACCGGTGCATCATCTTTGT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 14.10% | 8.20% | 11.87% | 65.85% | NA |
| All Indica | 2759 | 2.90% | 7.60% | 10.44% | 79.05% | NA |
| All Japonica | 1512 | 34.50% | 0.20% | 11.90% | 53.44% | NA |
| Aus | 269 | 14.50% | 59.10% | 17.84% | 8.55% | NA |
| Indica I | 595 | 5.20% | 5.40% | 7.39% | 82.02% | NA |
| Indica II | 465 | 3.90% | 17.40% | 2.80% | 75.91% | NA |
| Indica III | 913 | 0.50% | 4.10% | 13.58% | 81.82% | NA |
| Indica Intermediate | 786 | 3.40% | 7.50% | 13.61% | 75.45% | NA |
| Temperate Japonica | 767 | 58.90% | 0.00% | 1.96% | 39.11% | NA |
| Tropical Japonica | 504 | 3.20% | 0.20% | 27.58% | 69.05% | NA |
| Japonica Intermediate | 241 | 22.00% | 0.80% | 10.79% | 66.39% | NA |
| VI/Aromatic | 96 | 1.00% | 9.40% | 34.38% | 55.21% | NA |
| Intermediate | 90 | 27.80% | 6.70% | 13.33% | 52.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218655720 | A -> DEL | LOC_Os12g31040.1 | N | frameshift_variant | Average:22.365; most accessible tissue: Minghui63 root, score: 36.81 | N | N | N | N |
| vg1218655720 | A -> T | LOC_Os12g31040.1 | synonymous_variant ; p.Arg568Arg; LOW | synonymous_codon | Average:22.365; most accessible tissue: Minghui63 root, score: 36.81 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1218655720 | NA | 2.34E-07 | mr1163 | 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 |
| vg1218655720 | NA | 1.32E-06 | mr1521 | 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 |
| vg1218655720 | NA | 8.02E-06 | mr1708 | 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 |
| vg1218655720 | 3.51E-06 | 3.51E-06 | mr1812 | 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 |
| vg1218655720 | NA | 5.42E-07 | mr1851 | 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 |
| vg1218655720 | NA | 1.53E-09 | mr1486_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 |