| Variant ID: vg1018608957 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 18608957 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.06, others allele: 0.00, population size: 141. )
TATTTTGCAATTTTTTTGTTATTTAATAAGGATAATAAGCTAAAGGAGGCTGCAAAGATTGATTCATCATTTACAAGGTTTTCCACCAAGTATTTCTGTC[G/A]
AGTTATATCTGCACTTTCTCCACATCAGAAAACTATTATTCAGGGTGCTGGTTTTCAGAATTTGCTTGAGTTCAACAGCAATTATGTTCCAAATAAATTT
AAATTTATTTGGAACATAATTGCTGTTGAACTCAAGCAAATTCTGAAAACCAGCACCCTGAATAATAGTTTTCTGATGTGGAGAAAGTGCAGATATAACT[C/T]
GACAGAAATACTTGGTGGAAAACCTTGTAAATGATGAATCAATCTTTGCAGCCTCCTTTAGCTTATTATCCTTATTAAATAACAAAAAAATTGCAAAATA
| 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 | 73.00% | 4.60% | 1.27% | 21.12% | NA |
| All Indica | 2759 | 78.70% | 1.30% | 1.23% | 18.74% | NA |
| All Japonica | 1512 | 72.60% | 10.70% | 0.66% | 16.07% | NA |
| Aus | 269 | 30.10% | 1.10% | 3.35% | 65.43% | NA |
| Indica I | 595 | 85.00% | 1.30% | 2.18% | 11.43% | NA |
| Indica II | 465 | 81.90% | 0.00% | 1.08% | 16.99% | NA |
| Indica III | 913 | 75.90% | 1.50% | 0.55% | 22.02% | NA |
| Indica Intermediate | 786 | 75.20% | 1.90% | 1.40% | 21.50% | NA |
| Temperate Japonica | 767 | 95.70% | 0.40% | 0.26% | 3.65% | NA |
| Tropical Japonica | 504 | 33.10% | 30.20% | 1.19% | 35.52% | NA |
| Japonica Intermediate | 241 | 81.30% | 2.90% | 0.83% | 14.94% | NA |
| VI/Aromatic | 96 | 44.80% | 8.30% | 4.17% | 42.71% | NA |
| Intermediate | 90 | 66.70% | 6.70% | 3.33% | 23.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1018608957 | G -> A | LOC_Os10g34880.1 | missense_variant ; p.Arg105Gln; MODERATE | nonsynonymous_codon ; R105Q | Average:22.668; most accessible tissue: Callus, score: 54.557 | unknown | unknown | TOLERATED | 0.12 |
| vg1018608957 | G -> DEL | LOC_Os10g34880.1 | N | frameshift_variant | Average:22.668; most accessible tissue: Callus, score: 54.557 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1018608957 | 5.62E-10 | NA | mr1925 | 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 |
| vg1018608957 | NA | 1.75E-06 | mr1662_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 |