| Variant ID: vg0623252880 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 23252880 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ACATAGTCTTTGGGGACGATGGAAAGGGAAAAGTAATGGGATTGGGTAAGATTGCAATCTCCAATGATCTTTCCATTTCTAACGTTCTCTTGGTAAAATC[T/A]
CTAAACTATAATCTCTTGTCCGTTTCTCAATTATGTTCCATGGGCTACAATTGTCTTTTTACCGATGTTGATGTGACCGTATTTAGAAGGGATGACTCCT
AGGAGTCATCCCTTCTAAATACGGTCACATCAACATCGGTAAAAAGACAATTGTAGCCCATGGAACATAATTGAGAAACGGACAAGAGATTATAGTTTAG[A/T]
GATTTTACCAAGAGAACGTTAGAAATGGAAAGATCATTGGAGATTGCAATCTTACCCAATCCCATTACTTTTCCCTTTCCATCGTCCCCAAAGACTATGT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 57.50% | 14.50% | 26.64% | 1.35% | NA |
| All Indica | 2759 | 29.50% | 24.20% | 44.44% | 1.85% | NA |
| All Japonica | 1512 | 98.80% | 0.50% | 0.07% | 0.60% | NA |
| Aus | 269 | 94.80% | 0.40% | 4.83% | 0.00% | NA |
| Indica I | 595 | 10.40% | 23.00% | 65.71% | 0.84% | NA |
| Indica II | 465 | 56.60% | 25.40% | 17.63% | 0.43% | NA |
| Indica III | 913 | 24.20% | 22.20% | 49.40% | 4.16% | NA |
| Indica Intermediate | 786 | 34.20% | 26.60% | 38.42% | 0.76% | NA |
| Temperate Japonica | 767 | 98.30% | 0.80% | 0.00% | 0.91% | NA |
| Tropical Japonica | 504 | 99.40% | 0.20% | 0.20% | 0.20% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.40% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 3.12% | 0.00% | NA |
| Intermediate | 90 | 66.70% | 11.10% | 17.78% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0623252880 | T -> A | LOC_Os06g39160.1 | synonymous_variant ; p.Ser464Ser; LOW | synonymous_codon | Average:9.114; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |
| vg0623252880 | T -> DEL | LOC_Os06g39160.1 | N | frameshift_variant | Average:9.114; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0623252880 | NA | 4.44E-15 | mr1609 | 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 |
| vg0623252880 | NA | 1.88E-07 | mr1609 | 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 |
| vg0623252880 | NA | 7.64E-09 | mr1829 | 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 |
| vg0623252880 | NA | 4.04E-07 | mr1842 | 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 |
| vg0623252880 | NA | 1.52E-07 | mr1902 | 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 |
| vg0623252880 | NA | 2.44E-06 | mr1925_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 |