| Variant ID: vg0320737660 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 20737660 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
ACCAATAAAAGTTTTACAAAGCATGGCCAAAAAGTACAAGAGAGCTAAGACCCTACTCTTCAAAAAGAGGGAGGACGGACTCCCCCAGGTCGCCGACCTA[A/C]
TCCTTCACATCCTTGCGCACATCGCTGGCTGCCCCCTGATCCAAGATCTTCCGCAGATCGAGTTCAGGATGCGCCAGCCTCACACACGCAAGGACATGGC
GCCATGTCCTTGCGTGTGTGAGGCTGGCGCATCCTGAACTCGATCTGCGGAAGATCTTGGATCAGGGGGCAGCCAGCGATGTGCGCAAGGATGTGAAGGA[T/G]
TAGGTCGGCGACCTGGGGGAGTCCGTCCTCCCTCTTTTTGAAGAGTAGGGTCTTAGCTCTCTTGTACTTTTTGGCCATGCTTTGTAAAACTTTTATTGGT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 40.00% | 19.10% | 3.17% | 37.66% | NA |
| All Indica | 2759 | 7.60% | 29.30% | 3.73% | 59.41% | NA |
| All Japonica | 1512 | 94.90% | 2.60% | 1.46% | 1.06% | NA |
| Aus | 269 | 42.80% | 13.00% | 6.32% | 37.92% | NA |
| Indica I | 595 | 4.50% | 5.00% | 2.02% | 88.40% | NA |
| Indica II | 465 | 16.80% | 33.50% | 9.46% | 40.22% | NA |
| Indica III | 913 | 3.70% | 41.30% | 2.41% | 52.57% | NA |
| Indica Intermediate | 786 | 8.90% | 31.20% | 3.18% | 56.74% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.13% | 0.13% | NA |
| Tropical Japonica | 504 | 91.10% | 3.20% | 3.97% | 1.79% | NA |
| Japonica Intermediate | 241 | 87.60% | 9.50% | 0.41% | 2.49% | NA |
| VI/Aromatic | 96 | 76.00% | 14.60% | 6.25% | 3.12% | NA |
| Intermediate | 90 | 65.60% | 10.00% | 2.22% | 22.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0320737660 | A -> C | LOC_Os03g37411.1 | intron_variant ; MODIFIER | silent_mutation | Average:17.711; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
| vg0320737660 | A -> DEL | N | N | silent_mutation | Average:17.711; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0320737660 | NA | 7.59E-06 | mr1543 | Ind_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 |
| vg0320737660 | NA | 1.92E-08 | mr1543_2 | 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 |