| Variant ID: vg0416678941 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 16678941 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 82. )
TGTACTACCAAACAGTATCGTCGACCCCATCAACGATATTTGACCCGCTGTTGCCCGGAATCTTTTCTTCAGTTCTGGACTAACTCCATATATCTCAACT[C/T]
CTCATCAAGTCCCAGATATATCATGTTTCCACCGAATAATTCCATATGCAACCTGACTAGCCTGTTGCCGCCAGTCTACTCGCCCTTTGCACTTGCAAAC
GTTTGCAAGTGCAAAGGGCGAGTAGACTGGCGGCAACAGGCTAGTCAGGTTGCATATGGAATTATTCGGTGGAAACATGATATATCTGGGACTTGATGAG[G/A]
AGTTGAGATATATGGAGTTAGTCCAGAACTGAAGAAAAGATTCCGGGCAACAGCGGGTCAAATATCGTTGATGGGGTCGACGATACTGTTTGGTAGTACA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 72.80% | 12.00% | 15.02% | 0.17% | NA |
| All Indica | 2759 | 58.90% | 19.70% | 21.20% | 0.22% | NA |
| All Japonica | 1512 | 91.70% | 1.10% | 7.14% | 0.07% | NA |
| Aus | 269 | 97.80% | 0.70% | 1.49% | 0.00% | NA |
| Indica I | 595 | 65.40% | 15.50% | 19.16% | 0.00% | NA |
| Indica II | 465 | 43.70% | 31.20% | 25.16% | 0.00% | NA |
| Indica III | 913 | 63.60% | 17.00% | 18.84% | 0.55% | NA |
| Indica Intermediate | 786 | 57.50% | 19.20% | 23.16% | 0.13% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 76.40% | 3.00% | 20.44% | 0.20% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.80% | 2.07% | 0.00% | NA |
| VI/Aromatic | 96 | 96.90% | 1.00% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 80.00% | 6.70% | 12.22% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0416678941 | C -> DEL | N | N | silent_mutation | Average:36.041; most accessible tissue: Minghui63 flag leaf, score: 62.47 | N | N | N | N |
| vg0416678941 | C -> T | LOC_Os04g28220.1 | intron_variant ; MODIFIER | silent_mutation | Average:36.041; most accessible tissue: Minghui63 flag leaf, score: 62.47 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0416678941 | 2.01E-06 | 2.01E-06 | mr1370 | 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 |
| vg0416678941 | 5.66E-06 | 9.77E-06 | mr1398 | 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 |
| vg0416678941 | 2.09E-06 | 2.09E-06 | mr1463 | 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 |
| vg0416678941 | NA | 1.79E-07 | mr1584 | 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 |
| vg0416678941 | NA | 2.71E-06 | mr1866 | 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 |
| vg0416678941 | NA | 4.69E-06 | mr1498_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 |