| Variant ID: vg0817768586 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17768586 |
| Reference Allele: A | Alternative Allele: C,T |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.86, C: 0.14, others allele: 0.00, population size: 28. )
CGAGCGGTAAAAAAAAGTCAATTGTGTTACTTGTAATAATCATAGTCTAAGCAGGGGTTAAGATAAATCAAGTGTAGAGTGACATACAAGCAGGGAGCTA[A/C,T]
TCATTCTCATACTAAAATATCTAAGCTAAGTGGAAAGAAAATAGAAAGAGAATCTATTCCTATACTTCTAGTATACATAATATACATACATTCTAGTTAT
ATAACTAGAATGTATGTATATTATGTATACTAGAAGTATAGGAATAGATTCTCTTTCTATTTTCTTTCCACTTAGCTTAGATATTTTAGTATGAGAATGA[T/G,A]
TAGCTCCCTGCTTGTATGTCACTCTACACTTGATTTATCTTAACCCCTGCTTAGACTATGATTATTACAAGTAACACAATTGACTTTTTTTTACCGCTCG
| 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 | 32.20% | 10.80% | 3.22% | 53.75% | NA |
| All Indica | 2759 | 20.60% | 7.90% | 3.12% | 68.36% | NA |
| All Japonica | 1512 | 60.60% | 2.20% | 2.98% | 34.19% | NA |
| Aus | 269 | 3.70% | 86.60% | 1.12% | 8.55% | NA |
| Indica I | 595 | 37.10% | 3.20% | 3.87% | 55.80% | NA |
| Indica II | 465 | 26.70% | 11.00% | 4.09% | 58.28% | NA |
| Indica III | 913 | 2.20% | 8.00% | 2.85% | 86.97% | NA |
| Indica Intermediate | 786 | 25.80% | 9.70% | 2.29% | 62.21% | NA |
| Temperate Japonica | 767 | 83.30% | 0.30% | 1.69% | 14.73% | NA |
| Tropical Japonica | 504 | 35.10% | 5.00% | 3.77% | 56.15% | NA |
| Japonica Intermediate | 241 | 41.90% | 2.50% | 5.39% | 50.21% | NA |
| VI/Aromatic | 96 | 2.10% | 10.40% | 14.58% | 72.92% | NA |
| Intermediate | 90 | 30.00% | 16.70% | 4.44% | 48.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817768586 | A -> C | LOC_Os08g29020.1 | 3_prime_UTR_variant ; 1406.0bp to feature; MODIFIER | silent_mutation | Average:18.38; most accessible tissue: Callus, score: 78.505 | N | N | N | N |
| vg0817768586 | A -> T | LOC_Os08g29020.1 | 3_prime_UTR_variant ; 1406.0bp to feature; MODIFIER | N | Average:18.38; most accessible tissue: Callus, score: 78.505 | N | N | N | N |
| vg0817768586 | A -> DEL | N | N | silent_mutation | Average:18.38; most accessible tissue: Callus, score: 78.505 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0817768586 | NA | 4.29E-06 | mr1321_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 |
| vg0817768586 | 5.65E-08 | 3.44E-09 | mr1332_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 |
| vg0817768586 | 4.42E-06 | 1.29E-06 | mr1338_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 |
| vg0817768586 | NA | 4.70E-06 | mr1579_2 | 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 |