| Variant ID: vg0628634575 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 28634575 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 55. )
AAGCACGGCTAGTCCCCTACGGTGTTTCCGGATACTGTCAGGAGAGACGAAAGAGCTATCTCTGATCTCGCCGGGCACGGATTCGAGGAGAAAGGCTACC[C/T]
TGTTGTCGACTACGAGTCAGATCGTCAGACCGCCATGTCGACAACAGTTAGATAGGCTACCCCAAATATTGTACTAGTGTGATTATCATGAATAAGAGCA
TGCTCTTATTCATGATAATCACACTAGTACAATATTTGGGGTAGCCTATCTAACTGTTGTCGACATGGCGGTCTGACGATCTGACTCGTAGTCGACAACA[G/A]
GGTAGCCTTTCTCCTCGAATCCGTGCCCGGCGAGATCAGAGATAGCTCTTTCGTCTCTCCTGACAGTATCCGGAAACACCGTAGGGGACTAGCCGTGCTT
| 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 | 69.00% | 30.90% | 0.06% | 0.00% | NA |
| All Indica | 2759 | 49.10% | 50.80% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 66.70% | 33.30% | 0.00% | 0.00% | NA |
| Indica II | 465 | 18.90% | 80.90% | 0.22% | 0.00% | NA |
| Indica III | 913 | 49.40% | 50.50% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 53.40% | 46.60% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 97.70% | 2.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 91.70% | 8.30% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 63.30% | 35.60% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0628634575 | C -> T | LOC_Os06g47220.1 | upstream_gene_variant ; 4666.0bp to feature; MODIFIER | silent_mutation | Average:33.316; most accessible tissue: Zhenshan97 panicle, score: 63.607 | N | N | N | N |
| vg0628634575 | C -> T | LOC_Os06g47220-LOC_Os06g47230 | intergenic_region ; MODIFIER | silent_mutation | Average:33.316; most accessible tissue: Zhenshan97 panicle, score: 63.607 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0628634575 | 2.84E-06 | 2.84E-06 | mr1760_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 |
| vg0628634575 | NA | 4.25E-07 | mr1974_2 | 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 |
| vg0628634575 | NA | 8.32E-07 | mr1974_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 |