| Variant ID: vg0611847509 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 11847509 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CCCGAGAGCATGTAGCCTTTTTGCTCATGTGGCTAGAAAAATTCCTCTTCTGTGGATCCAGTTGTGGCCCCACAACCAACTGGCAATTTGTAGCCGAAGC[C/T]
CTGGAATCAAAGAAAGAATTCCCTTTGGGAAAAATTCTTCTCGGCTACCTGTACCAGATGTTAAACAATGCATCGGCTAGAATTGCCGTCAGCTCGGCAG
CTGCCGAGCTGACGGCAATTCTAGCCGATGCATTGTTTAACATCTGGTACAGGTAGCCGAGAAGAATTTTTCCCAAAGGGAATTCTTTCTTTGATTCCAG[G/A]
GCTTCGGCTACAAATTGCCAGTTGGTTGTGGGGCCACAACTGGATCCACAGAAGAGGAATTTTTCTAGCCACATGAGCAAAAAGGCTACATGCTCTCGGG
| 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 | 84.40% | 1.80% | 4.51% | 9.33% | NA |
| All Indica | 2759 | 78.60% | 0.40% | 6.63% | 14.35% | NA |
| All Japonica | 1512 | 93.10% | 4.70% | 1.32% | 0.93% | NA |
| Aus | 269 | 89.60% | 0.00% | 2.97% | 7.43% | NA |
| Indica I | 595 | 81.00% | 0.00% | 4.20% | 14.79% | NA |
| Indica II | 465 | 66.50% | 0.40% | 8.82% | 24.30% | NA |
| Indica III | 913 | 84.30% | 0.00% | 7.23% | 8.43% | NA |
| Indica Intermediate | 786 | 77.20% | 1.30% | 6.49% | 15.01% | NA |
| Temperate Japonica | 767 | 98.40% | 0.40% | 0.65% | 0.52% | NA |
| Tropical Japonica | 504 | 83.10% | 13.30% | 2.38% | 1.19% | NA |
| Japonica Intermediate | 241 | 96.70% | 0.40% | 1.24% | 1.66% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 83.30% | 2.20% | 2.22% | 12.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0611847509 | C -> T | LOC_Os06g20580.1 | synonymous_variant ; p.Ala233Ala; LOW | synonymous_codon | Average:24.379; most accessible tissue: Zhenshan97 root, score: 38.035 | N | N | N | N |
| vg0611847509 | C -> DEL | LOC_Os06g20580.1 | N | frameshift_variant | Average:24.379; most accessible tissue: Zhenshan97 root, score: 38.035 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0611847509 | NA | 3.52E-06 | mr1676 | 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 |
| vg0611847509 | NA | 3.02E-07 | mr1951 | 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 |
| vg0611847509 | 1.99E-07 | 1.23E-11 | mr1676_2 | 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 |