| Variant ID: vg0222211789 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 22211789 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 99. )
GTCCATGCTCGCTCCGTACCTCTACCCCCCACTGCCGTGAGCCACCGCCGTCGTCCCCTTAGTCCTCCCATTACCGTGAGCCTCCGCGGCCGAGCCGCCG[C/T]
CCCTGGTTCTGCTGCGCCCCCATGCCGCCGACCGCTGCTGCCAACAAAGGAAGATAGAGTATAGGAGGGGAGTCGCTGACAGGTGGGTCCCACTTTATTT
AAATAAAGTGGGACCCACCTGTCAGCGACTCCCCTCCTATACTCTATCTTCCTTTGTTGGCAGCAGCGGTCGGCGGCATGGGGGCGCAGCAGAACCAGGG[G/A]
CGGCGGCTCGGCCGCGGAGGCTCACGGTAATGGGAGGACTAAGGGGACGACGGCGGTGGCTCACGGCAGTGGGGGGTAGAGGTACGGAGCGAGCATGGAC
| 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 | 34.90% | 15.00% | 1.14% | 48.92% | NA |
| All Indica | 2759 | 5.30% | 24.90% | 1.70% | 68.07% | NA |
| All Japonica | 1512 | 93.00% | 0.70% | 0.13% | 6.22% | NA |
| Aus | 269 | 0.00% | 0.70% | 0.37% | 98.88% | NA |
| Indica I | 595 | 4.50% | 28.10% | 1.34% | 66.05% | NA |
| Indica II | 465 | 1.50% | 8.40% | 3.01% | 87.10% | NA |
| Indica III | 913 | 3.90% | 32.40% | 0.33% | 63.31% | NA |
| Indica Intermediate | 786 | 9.70% | 23.70% | 2.80% | 63.87% | NA |
| Temperate Japonica | 767 | 98.30% | 0.10% | 0.13% | 1.43% | NA |
| Tropical Japonica | 504 | 83.50% | 1.60% | 0.20% | 14.68% | NA |
| Japonica Intermediate | 241 | 95.90% | 0.40% | 0.00% | 3.73% | NA |
| VI/Aromatic | 96 | 60.40% | 1.00% | 0.00% | 38.54% | NA |
| Intermediate | 90 | 44.40% | 10.00% | 4.44% | 41.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0222211789 | C -> T | LOC_Os02g36830.1 | upstream_gene_variant ; 3268.0bp to feature; MODIFIER | silent_mutation | Average:19.146; most accessible tissue: Callus, score: 94.658 | N | N | N | N |
| vg0222211789 | C -> T | LOC_Os02g36820.1 | downstream_gene_variant ; 61.0bp to feature; MODIFIER | silent_mutation | Average:19.146; most accessible tissue: Callus, score: 94.658 | N | N | N | N |
| vg0222211789 | C -> T | LOC_Os02g36820-LOC_Os02g36830 | intergenic_region ; MODIFIER | silent_mutation | Average:19.146; most accessible tissue: Callus, score: 94.658 | N | N | N | N |
| vg0222211789 | C -> DEL | N | N | silent_mutation | Average:19.146; most accessible tissue: Callus, score: 94.658 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0222211789 | 8.50E-06 | 5.68E-06 | mr1080 | 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 |
| vg0222211789 | 2.47E-06 | 2.47E-06 | mr1255 | 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 |
| vg0222211789 | 2.77E-07 | 3.64E-09 | mr1619 | 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 |