| Variant ID: vg0510636377 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 10636377 |
| 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: 241. )
GAAAAAACACTAATAAAAACCAAATAAACAGTACAATTAAAGTTCACAAATAGGTAGAGCTTGAATTCAGATGAATTATGAGACTTGAACGACCTCATTC[C/T]
GAGTTCGTATGAATTAGATATGAATTTTACAAGATTTAATTCCAATTAAACCTATTAAAGAAAAGACTATTCCAAATTGATTAAACAATTTACAAATGAC
GTCATTTGTAAATTGTTTAATCAATTTGGAATAGTCTTTTCTTTAATAGGTTTAATTGGAATTAAATCTTGTAAAATTCATATCTAATTCATACGAACTC[G/A]
GAATGAGGTCGTTCAAGTCTCATAATTCATCTGAATTCAAGCTCTACCTATTTGTGAACTTTAATTGTACTGTTTATTTGGTTTTTATTAGTGTTTTTTC
| 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 | 90.90% | 7.50% | 1.61% | 0.00% | NA |
| All Indica | 2759 | 91.00% | 6.20% | 2.75% | 0.00% | NA |
| All Japonica | 1512 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 36.10% | 63.90% | 0.00% | 0.00% | NA |
| Indica I | 595 | 92.40% | 0.00% | 7.56% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.40% | 0.43% | 0.00% | NA |
| Indica III | 913 | 83.00% | 15.40% | 1.53% | 0.00% | NA |
| Indica Intermediate | 786 | 94.40% | 3.70% | 1.91% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 7.80% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0510636377 | C -> T | LOC_Os05g18400.1 | downstream_gene_variant ; 1351.0bp to feature; MODIFIER | silent_mutation | Average:18.817; most accessible tissue: Zhenshan97 panicle, score: 28.447 | N | N | N | N |
| vg0510636377 | C -> T | LOC_Os05g18390-LOC_Os05g18400 | intergenic_region ; MODIFIER | silent_mutation | Average:18.817; most accessible tissue: Zhenshan97 panicle, score: 28.447 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0510636377 | NA | 7.11E-06 | mr1230 | 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 |
| vg0510636377 | 4.96E-06 | NA | mr1304_2 | 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 |
| vg0510636377 | 6.16E-06 | NA | 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 |