| Variant ID: vg0320735515 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 20735515 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
ACCCACGGGGGAAATCAAGGCTGACAACGCTATCAAATTCATCAAAGGGATATTCTGCAGATTCGGATTGCCCCACCGTATCATAACGGACAACGGCTCC[T/C]
AGTTCATCAGTGCATATTTCCAGGATTACTGCATCAGGCTGGGAGTCAAGATCTGCTTCGCCTCAGTCTCTCACCCTCAGAGCAATGGACAAGTCGAGAG
CTCTCGACTTGTCCATTGCTCTGAGGGTGAGAGACTGAGGCGAAGCAGATCTTGACTCCCAGCCTGATGCAGTAATCCTGGAAATATGCACTGATGAACT[A/G]
GGAGCCGTTGTCCGTTATGATACGGTGGGGCAATCCGAATCTGCAGAATATCCCTTTGATGAATTTGATAGCGTTGTCAGCCTTGATTTCCCCCGTGGGT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 34.80% | 0.20% | 7.85% | 57.17% | NA |
| All Indica | 2759 | 5.40% | 0.20% | 5.87% | 88.51% | NA |
| All Japonica | 1512 | 87.90% | 0.20% | 7.14% | 4.76% | NA |
| Aus | 269 | 14.50% | 0.70% | 29.74% | 55.02% | NA |
| Indica I | 595 | 5.90% | 0.50% | 1.34% | 92.27% | NA |
| Indica II | 465 | 6.70% | 0.00% | 18.71% | 74.62% | NA |
| Indica III | 913 | 2.50% | 0.00% | 3.29% | 94.19% | NA |
| Indica Intermediate | 786 | 7.80% | 0.30% | 4.71% | 87.28% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.13% | 0.13% | NA |
| Tropical Japonica | 504 | 67.70% | 0.60% | 20.24% | 11.51% | NA |
| Japonica Intermediate | 241 | 92.50% | 0.00% | 2.07% | 5.39% | NA |
| VI/Aromatic | 96 | 76.00% | 0.00% | 10.42% | 13.54% | NA |
| Intermediate | 90 | 57.80% | 0.00% | 12.22% | 30.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0320735515 | T -> C | LOC_Os03g37411.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.941; most accessible tissue: Callus, score: 20.089 | N | N | N | N |
| vg0320735515 | T -> DEL | N | N | silent_mutation | Average:6.941; most accessible tissue: Callus, score: 20.089 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0320735515 | NA | 1.78E-09 | mr1136 | 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 |
| vg0320735515 | NA | 3.38E-10 | mr1188 | 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 |
| vg0320735515 | NA | 2.82E-06 | mr1583 | 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 |
| vg0320735515 | NA | 2.40E-11 | mr1188_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 |
| vg0320735515 | NA | 5.28E-07 | mr1218_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 |
| vg0320735515 | NA | 2.07E-09 | mr1850_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 |