| Variant ID: vg0217649884 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 17649884 |
| 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: 96. )
TGGGAGTCCACGCCTCTGGTTATTGAGGGGGTGATTATGATCCAGGAATGGTGCACTGTGGTGGATTGTGTTGTGCAAGGGGTACTGTCACAGTTCCTAT[C/T]
TGAGATATCGTGGTGGTATTGAGGCGCATGGTAACATGTTGTGGAGCTGTGTCTTGTGGGTACAGTGGTACATCTCTGGCCAGAGTAAAACTATTCGAAT
ATTCGAATAGTTTTACTCTGGCCAGAGATGTACCACTGTACCCACAAGACACAGCTCCACAACATGTTACCATGCGCCTCAATACCACCACGATATCTCA[G/A]
ATAGGAACTGTGACAGTACCCCTTGCACAACACAATCCACCACAGTGCACCATTCCTGGATCATAATCACCCCCTCAATAACCAGAGGCGTGGACTCCCA
| 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 | 39.50% | 6.70% | 28.99% | 24.86% | NA |
| All Indica | 2759 | 11.30% | 11.30% | 45.96% | 31.42% | NA |
| All Japonica | 1512 | 98.20% | 0.00% | 1.06% | 0.73% | NA |
| Aus | 269 | 3.30% | 0.40% | 5.20% | 91.08% | NA |
| Indica I | 595 | 8.20% | 1.30% | 38.82% | 51.60% | NA |
| Indica II | 465 | 15.70% | 4.10% | 60.00% | 20.22% | NA |
| Indica III | 913 | 12.00% | 25.30% | 37.13% | 25.52% | NA |
| Indica Intermediate | 786 | 10.30% | 6.70% | 53.31% | 29.64% | NA |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.91% | 0.52% | NA |
| Tropical Japonica | 504 | 98.20% | 0.00% | 0.99% | 0.79% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.00% | 1.66% | 1.24% | NA |
| VI/Aromatic | 96 | 15.60% | 3.10% | 58.33% | 22.92% | NA |
| Intermediate | 90 | 47.80% | 1.10% | 17.78% | 33.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0217649884 | C -> T | LOC_Os02g29650.1 | upstream_gene_variant ; 1819.0bp to feature; MODIFIER | silent_mutation | Average:37.358; most accessible tissue: Minghui63 young leaf, score: 80.562 | N | N | N | N |
| vg0217649884 | C -> T | LOC_Os02g29640-LOC_Os02g29650 | intergenic_region ; MODIFIER | silent_mutation | Average:37.358; most accessible tissue: Minghui63 young leaf, score: 80.562 | N | N | N | N |
| vg0217649884 | C -> DEL | N | N | silent_mutation | Average:37.358; most accessible tissue: Minghui63 young leaf, score: 80.562 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0217649884 | NA | 2.43E-07 | mr1093 | 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 |
| vg0217649884 | NA | 3.17E-28 | mr1546 | 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 |
| vg0217649884 | NA | 1.82E-06 | mr1064_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 |
| vg0217649884 | 8.21E-07 | NA | mr1134_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 |
| vg0217649884 | NA | 5.66E-23 | mr1386_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 |