| Variant ID: vg1206482579 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 6482579 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
ATTTCCCCAGTGGGTACTGCTTCGATCCATTTGGTGAATTTGTCGATTGCCACAAATAGGAATCTGTAGCCGCCCTGTCCTCGTGGGAATGGCCCAAGTA[T/G]
ATCTAGCCCCCAGCATGAGAACGGCCAAGTCAGAGGGATAGTCTGGAGCGCTTGCGCAGGTAGCTTTGTGTGTTTACTGTGAAATTGACAGGCTTCACAT
ATGTGAAGCCTGTCAATTTCACAGTAAACACACAAAGCTACCTGCGCAAGCGCTCCAGACTATCCCTCTGACTTGGCCGTTCTCATGCTGGGGGCTAGAT[A/C]
TACTTGGGCCATTCCCACGAGGACAGGGCGGCTACAGATTCCTATTTGTGGCAATCGACAAATTCACCAAATGGATCGAAGCAGTACCCACTGGGGAAAT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 57.00% | 0.40% | 3.68% | 38.89% | NA |
| All Indica | 2759 | 57.00% | 0.40% | 4.42% | 38.20% | NA |
| All Japonica | 1512 | 51.90% | 0.70% | 2.51% | 44.91% | NA |
| Aus | 269 | 77.30% | 0.00% | 1.12% | 21.56% | NA |
| Indica I | 595 | 45.00% | 0.00% | 9.92% | 45.04% | NA |
| Indica II | 465 | 82.20% | 0.40% | 1.72% | 15.70% | NA |
| Indica III | 913 | 49.40% | 0.50% | 2.41% | 47.65% | NA |
| Indica Intermediate | 786 | 60.10% | 0.40% | 4.20% | 35.37% | NA |
| Temperate Japonica | 767 | 62.70% | 0.30% | 1.17% | 35.85% | NA |
| Tropical Japonica | 504 | 31.90% | 1.40% | 5.36% | 61.31% | NA |
| Japonica Intermediate | 241 | 58.90% | 0.80% | 0.83% | 39.42% | NA |
| VI/Aromatic | 96 | 75.00% | 0.00% | 4.17% | 20.83% | NA |
| Intermediate | 90 | 62.20% | 0.00% | 7.78% | 30.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1206482579 | T -> DEL | N | N | silent_mutation | Average:8.125; most accessible tissue: Minghui63 young leaf, score: 14.915 | N | N | N | N |
| vg1206482579 | T -> G | LOC_Os12g11900.1 | 3_prime_UTR_variant ; 516.0bp to feature; MODIFIER | silent_mutation | Average:8.125; most accessible tissue: Minghui63 young leaf, score: 14.915 | N | N | N | N |
| vg1206482579 | T -> G | LOC_Os12g11890.1 | downstream_gene_variant ; 1519.0bp to feature; MODIFIER | silent_mutation | Average:8.125; most accessible tissue: Minghui63 young leaf, score: 14.915 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1206482579 | NA | 7.63E-06 | mr1379_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 |
| vg1206482579 | 3.35E-06 | 1.44E-07 | mr1633_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 |
| vg1206482579 | 6.50E-07 | 6.50E-07 | mr1649_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 |