| Variant ID: vg0915760236 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 15760236 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TTCTAGGTGCAATAGGTTGCTAAATAGTACTCGAGAAAATCTCTTGTGTACCCCTGAAAGTTCACCTAATCCCTTCTGTACCCCTGAATTTTGCTCAATC[T/C]
CTTATATACCCCTGAATTTTAATTTGGATCCCTTCCATGCCCTTTCCGCTAGTTGACCGTTAGTTGACCGTTAAATTCTTATGAAAAAGTCTATTTTTCC
GGAAAAATAGACTTTTTCATAAGAATTTAACGGTCAACTAACGGTCAACTAGCGGAAAGGGCATGGAAGGGATCCAAATTAAAATTCAGGGGTATATAAG[A/G]
GATTGAGCAAAATTCAGGGGTACAGAAGGGATTAGGTGAACTTTCAGGGGTACACAAGAGATTTTCTCGAGTACTATTTAGCAACCTATTGCACCTAGAA
| 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 | 56.90% | 34.30% | 6.75% | 2.07% | NA |
| All Indica | 2759 | 84.50% | 1.20% | 10.91% | 3.48% | NA |
| All Japonica | 1512 | 1.00% | 98.50% | 0.46% | 0.07% | NA |
| Aus | 269 | 97.00% | 1.50% | 1.12% | 0.37% | NA |
| Indica I | 595 | 84.50% | 0.50% | 12.77% | 2.18% | NA |
| Indica II | 465 | 81.70% | 1.90% | 9.89% | 6.45% | NA |
| Indica III | 913 | 89.20% | 0.50% | 5.91% | 4.38% | NA |
| Indica Intermediate | 786 | 80.50% | 1.90% | 15.90% | 1.65% | NA |
| Temperate Japonica | 767 | 0.40% | 99.50% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 1.00% | 98.00% | 0.79% | 0.20% | NA |
| Japonica Intermediate | 241 | 2.90% | 96.30% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 51.00% | 49.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 38.90% | 52.20% | 8.89% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0915760236 | T -> DEL | N | N | silent_mutation | Average:24.837; most accessible tissue: Callus, score: 37.948 | N | N | N | N |
| vg0915760236 | T -> C | LOC_Os09g26144.1 | intron_variant ; MODIFIER | silent_mutation | Average:24.837; most accessible tissue: Callus, score: 37.948 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0915760236 | NA | 1.84E-07 | mr1717 | 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 |
| vg0915760236 | 2.13E-07 | 2.13E-07 | mr1717 | 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 |