| Variant ID: vg0139977615 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 39977615 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 336. )
ACCTAGGCATCTATCTTATTCCACAGGCGAGGCTTGGGGCTAGGCACGAAACATCTAGAAGTCTTCATACTCGGCTTGCTCCTGGAGATACTCCTTGGCG[G/A]
TCGGGTCGATGTCTTCATCTCCATACTCTATATAATATTATAAGGGGCAAGGGTGAGTACTTAACGTACTCAGCAAGCCAGGGGAAAGAATGACATGTTT
AAACATGTCATTCTTTCCCCTGGCTTGCTGAGTACGTTAAGTACTCACCCTTGCCCCTTATAATATTATATAGAGTATGGAGATGAAGACATCGACCCGA[C/T]
CGCCAAGGAGTATCTCCAGGAGCAAGCCGAGTATGAAGACTTCTAGATGTTTCGTGCCTAGCCCCAAGCCTCGCCTGTGGAATAAGATAGATGCCTAGGT
| 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 | 90.60% | 6.40% | 1.88% | 1.12% | NA |
| All Indica | 2759 | 96.20% | 0.20% | 1.85% | 1.74% | NA |
| All Japonica | 1512 | 79.60% | 19.00% | 1.26% | 0.07% | NA |
| Aus | 269 | 93.70% | 0.00% | 5.95% | 0.37% | NA |
| Indica I | 595 | 97.50% | 0.20% | 1.34% | 1.01% | NA |
| Indica II | 465 | 90.50% | 0.40% | 5.59% | 3.44% | NA |
| Indica III | 913 | 98.60% | 0.00% | 0.22% | 1.20% | NA |
| Indica Intermediate | 786 | 95.80% | 0.40% | 1.91% | 1.91% | NA |
| Temperate Japonica | 767 | 76.80% | 22.90% | 0.13% | 0.13% | NA |
| Tropical Japonica | 504 | 85.90% | 10.70% | 3.37% | 0.00% | NA |
| Japonica Intermediate | 241 | 75.50% | 24.10% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 84.40% | 10.00% | 3.33% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0139977615 | G -> A | LOC_Os01g68810.1 | upstream_gene_variant ; 1698.0bp to feature; MODIFIER | silent_mutation | Average:38.308; most accessible tissue: Zhenshan97 root, score: 62.394 | N | N | N | N |
| vg0139977615 | G -> A | LOC_Os01g68810-LOC_Os01g68820 | intergenic_region ; MODIFIER | silent_mutation | Average:38.308; most accessible tissue: Zhenshan97 root, score: 62.394 | N | N | N | N |
| vg0139977615 | G -> DEL | N | N | silent_mutation | Average:38.308; most accessible tissue: Zhenshan97 root, score: 62.394 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0139977615 | 1.18E-06 | NA | mr1154 | 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 |
| vg0139977615 | 2.01E-06 | 1.79E-07 | mr1154 | 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 |
| vg0139977615 | 3.05E-06 | NA | mr1092_2 | 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 |
| vg0139977615 | 3.46E-06 | 5.92E-07 | mr1092_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 |
| vg0139977615 | NA | 6.78E-06 | mr1555_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 |