| Variant ID: vg0623427584 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 23427584 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.77, G: 0.23, others allele: 0.00, population size: 47. )
TTGCCATGATCACTGTCAGGAAGTCAGGACGATCTTTCTTGGAATGTCTTGTCTTCTTGCAGTGGAGACACTGATCCTGTCTCAACTGTGAACTGTTGTT[G/T]
CTGAGGCAGATGCTGAGGCTGTTTTGCTTTTGAGGAGGGTGACCCGTGGCTCTTTTCCTTGTTATCTTTAACAAGGTTAATGGAGCCACCATTGGTCTCT
AGAGACCAATGGTGGCTCCATTAACCTTGTTAAAGATAACAAGGAAAAGAGCCACGGGTCACCCTCCTCAAAAGCAAAACAGCCTCAGCATCTGCCTCAG[C/A]
AACAACAGTTCACAGTTGAGACAGGATCAGTGTCTCCACTGCAAGAAGACAAGACATTCCAAGAAAGATCGTCCTGACTTCCTGACAGTGATCATGGCAA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 12.40% | 8.50% | 7.32% | 71.75% | NA |
| All Indica | 2759 | 20.10% | 2.30% | 10.98% | 66.65% | NA |
| All Japonica | 1512 | 0.30% | 20.40% | 1.59% | 77.78% | NA |
| Aus | 269 | 8.90% | 2.60% | 2.60% | 85.87% | NA |
| Indica I | 595 | 18.80% | 1.80% | 10.76% | 68.57% | NA |
| Indica II | 465 | 16.10% | 5.80% | 13.98% | 64.09% | NA |
| Indica III | 913 | 27.40% | 0.30% | 9.86% | 62.43% | NA |
| Indica Intermediate | 786 | 14.90% | 2.80% | 10.69% | 71.63% | NA |
| Temperate Japonica | 767 | 0.30% | 34.20% | 1.43% | 64.15% | NA |
| Tropical Japonica | 504 | 0.40% | 4.60% | 0.99% | 94.05% | NA |
| Japonica Intermediate | 241 | 0.00% | 9.50% | 3.32% | 87.14% | NA |
| VI/Aromatic | 96 | 2.10% | 8.30% | 1.04% | 88.54% | NA |
| Intermediate | 90 | 4.40% | 16.70% | 12.22% | 66.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0623427584 | G -> T | LOC_Os06g39450.1 | missense_variant ; p.Ser259Arg; MODERATE | nonsynonymous_codon ; S259R | Average:10.762; most accessible tissue: Zhenshan97 panicle, score: 28.447 | unknown | unknown | TOLERATED | 0.48 |
| vg0623427584 | G -> DEL | LOC_Os06g39450.1 | N | frameshift_variant | Average:10.762; most accessible tissue: Zhenshan97 panicle, score: 28.447 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0623427584 | NA | 9.87E-06 | mr1011 | 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 |
| vg0623427584 | NA | 7.22E-08 | mr1162 | 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 |
| vg0623427584 | 6.07E-07 | NA | mr1176 | 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 |
| vg0623427584 | NA | 1.12E-06 | mr1295 | 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 |
| vg0623427584 | NA | 1.34E-06 | mr1536 | 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 |
| vg0623427584 | 4.80E-07 | 4.35E-06 | mr1792 | 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 |