| Variant ID: vg0414098504 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 14098504 |
| Reference Allele: C | Alternative Allele: T,A |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.64, T: 0.36, others allele: 0.00, population size: 105. )
CCCACATGGGCCCCACTTGGGCCAGGGTCCCAAACGAAGTTACAAGCCCAAAGGCCCATGACAGGTAACACAGCACCTTGTTTTTGTGTTTGCGGCCAAA[C/T,A]
GATATGGAGTTTGGTGATGAGGCTGGATCCGTTAGAAAGAGGACTCTGAGAGCTTTCCATCAAGTACTCATGGGCTGAAAACGGAGGTCGTATGCAGATT
AATCTGCATACGACCTCCGTTTTCAGCCCATGAGTACTTGATGGAAAGCTCTCAGAGTCCTCTTTCTAACGGATCCAGCCTCATCACCAAACTCCATATC[G/A,T]
TTTGGCCGCAAACACAAAAACAAGGTGCTGTGTTACCTGTCATGGGCCTTTGGGCTTGTAACTTCGTTTGGGACCCTGGCCCAAGTGGGGCCCATGTGGG
| 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 | 67.00% | 32.70% | 0.08% | 0.00% | A: 0.23% |
| All Indica | 2759 | 54.20% | 45.50% | 0.11% | 0.00% | A: 0.18% |
| All Japonica | 1512 | 87.00% | 13.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 92.60% | 4.80% | 0.37% | 0.00% | A: 2.23% |
| Indica I | 595 | 51.40% | 48.60% | 0.00% | 0.00% | NA |
| Indica II | 465 | 72.70% | 27.10% | 0.22% | 0.00% | NA |
| Indica III | 913 | 47.20% | 52.40% | 0.11% | 0.00% | A: 0.33% |
| Indica Intermediate | 786 | 53.60% | 46.10% | 0.13% | 0.00% | A: 0.25% |
| Temperate Japonica | 767 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 83.50% | 16.50% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 63.10% | 36.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 49.00% | 51.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 64.40% | 35.60% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0414098504 | C -> A | LOC_Os04g24550.1 | downstream_gene_variant ; 3409.0bp to feature; MODIFIER | silent_mutation | Average:55.226; most accessible tissue: Zhenshan97 panicle, score: 68.538 | N | N | N | N |
| vg0414098504 | C -> A | LOC_Os04g24560.1 | downstream_gene_variant ; 749.0bp to feature; MODIFIER | silent_mutation | Average:55.226; most accessible tissue: Zhenshan97 panicle, score: 68.538 | N | N | N | N |
| vg0414098504 | C -> A | LOC_Os04g24550-LOC_Os04g24560 | intergenic_region ; MODIFIER | silent_mutation | Average:55.226; most accessible tissue: Zhenshan97 panicle, score: 68.538 | N | N | N | N |
| vg0414098504 | C -> T | LOC_Os04g24550.1 | downstream_gene_variant ; 3409.0bp to feature; MODIFIER | silent_mutation | Average:55.226; most accessible tissue: Zhenshan97 panicle, score: 68.538 | N | N | N | N |
| vg0414098504 | C -> T | LOC_Os04g24560.1 | downstream_gene_variant ; 749.0bp to feature; MODIFIER | silent_mutation | Average:55.226; most accessible tissue: Zhenshan97 panicle, score: 68.538 | N | N | N | N |
| vg0414098504 | C -> T | LOC_Os04g24550-LOC_Os04g24560 | intergenic_region ; MODIFIER | silent_mutation | Average:55.226; most accessible tissue: Zhenshan97 panicle, score: 68.538 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0414098504 | NA | 5.83E-06 | mr1037 | 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 |
| vg0414098504 | NA | 4.68E-06 | mr1066 | 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 |
| vg0414098504 | NA | 2.81E-06 | mr1280 | 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 |
| vg0414098504 | 5.40E-06 | NA | mr1584 | 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 |
| vg0414098504 | 2.54E-06 | 2.54E-06 | mr1584 | 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 |
| vg0414098504 | NA | 1.70E-06 | mr1729 | 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 |
| vg0414098504 | NA | 6.90E-06 | mr1788 | 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 |
| vg0414098504 | NA | 8.09E-06 | mr1380_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 |
| vg0414098504 | 4.75E-06 | 4.74E-06 | mr1651_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 |
| vg0414098504 | NA | 1.18E-06 | mr1655_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 |
| vg0414098504 | NA | 8.46E-06 | mr1669_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 |
| vg0414098504 | NA | 7.52E-06 | mr1682_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 |