| Variant ID: vg0403938051 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 3938051 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.02, others allele: 0.00, population size: 117. )
CGCGCACCCTACGCCGAACTCATTATGCTCGGTGATGGGACTAGGGCCACCAGATGGCGAAATAATCTGGCAGACCCCTTCAACAAAGGGACCGATCTCC[G/A]
GTCGGGAGGTGAAGTCGGCAGAGACAAACTGGGGCGCGGTGAGTGTCATATCAGACACTGTCATTTAGATCGCCACTGCCTGGCCCTCTCGCTGGCGACT
AGTCGCCAGCGAGAGGGCCAGGCAGTGGCGATCTAAATGACAGTGTCTGATATGACACTCACCGCGCCCCAGTTTGTCTCTGCCGACTTCACCTCCCGAC[C/T]
GGAGATCGGTCCCTTTGTTGAAGGGGTCTGCCAGATTATTTCGCCATCTGGTGGCCCTAGTCCCATCACCGAGCATAATGAGTTCGGCGTAGGGTGCGCG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 54.50% | 32.40% | 8.74% | 4.32% | NA |
| All Indica | 2759 | 32.60% | 50.40% | 11.16% | 5.87% | NA |
| All Japonica | 1512 | 90.70% | 6.50% | 1.32% | 1.52% | NA |
| Aus | 269 | 73.60% | 3.30% | 19.33% | 3.72% | NA |
| Indica I | 595 | 2.20% | 97.10% | 0.50% | 0.17% | NA |
| Indica II | 465 | 35.30% | 48.80% | 12.04% | 3.87% | NA |
| Indica III | 913 | 53.10% | 22.70% | 12.81% | 11.39% | NA |
| Indica Intermediate | 786 | 30.20% | 48.10% | 16.79% | 4.96% | NA |
| Temperate Japonica | 767 | 99.10% | 0.30% | 0.39% | 0.26% | NA |
| Tropical Japonica | 504 | 76.60% | 17.10% | 2.58% | 3.77% | NA |
| Japonica Intermediate | 241 | 93.40% | 4.10% | 1.66% | 0.83% | NA |
| VI/Aromatic | 96 | 64.60% | 6.20% | 22.92% | 6.25% | NA |
| Intermediate | 90 | 53.30% | 31.10% | 12.22% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0403938051 | G -> DEL | LOC_Os04g07390.1 | N | frameshift_variant | Average:60.412; most accessible tissue: Zhenshan97 young leaf, score: 83.412 | N | N | N | N |
| vg0403938051 | G -> A | LOC_Os04g07390.1 | missense_variant ; p.Gly55Ser; MODERATE | nonsynonymous_codon ; G55S | Average:60.412; most accessible tissue: Zhenshan97 young leaf, score: 83.412 | unknown | unknown | DELETERIOUS | 0.00 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0403938051 | 3.76E-06 | 2.06E-07 | mr1332 | 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 |
| vg0403938051 | NA | 1.28E-06 | mr1727_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 |
| vg0403938051 | NA | 1.14E-07 | mr1837_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 |
| vg0403938051 | NA | 8.51E-07 | mr1915_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 |