| Variant ID: vg0141980593 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 41980593 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TTCATAACTTTTTCAAATAAGACGGACGGTCAAACATTGGGATGCGGCTTCCCTGTTCCTATGTTATGTTCCCCTCCCTGTCCCCTGCAAGATGTCCTCC[C/T]
TCTATTGGCTGCTGCTTTTCTAGTGGACCCAGGCCATGCGCTCGTTTTCTTTTTTAACGTAAACGACGTTAACATCCGGGATGGCTCGTTTCTGAGCAAG
CTTGCTCAGAAACGAGCCATCCCGGATGTTAACGTCGTTTACGTTAAAAAAGAAAACGAGCGCATGGCCTGGGTCCACTAGAAAAGCAGCAGCCAATAGA[G/A]
GGAGGACATCTTGCAGGGGACAGGGAGGGGAACATAACATAGGAACAGGGAAGCCGCATCCCAATGTTTGACCGTCCGTCTTATTTGAAAAAGTTATGAA
| 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 | 85.00% | 5.30% | 0.74% | 8.95% | NA |
| All Indica | 2759 | 77.10% | 8.70% | 1.05% | 13.19% | NA |
| All Japonica | 1512 | 95.80% | 0.30% | 0.40% | 3.57% | NA |
| Aus | 269 | 98.10% | 1.90% | 0.00% | 0.00% | NA |
| Indica I | 595 | 68.20% | 14.80% | 1.18% | 15.80% | NA |
| Indica II | 465 | 89.00% | 1.10% | 1.29% | 8.60% | NA |
| Indica III | 913 | 76.00% | 11.40% | 0.55% | 12.05% | NA |
| Indica Intermediate | 786 | 77.90% | 5.50% | 1.40% | 15.27% | NA |
| Temperate Japonica | 767 | 99.50% | 0.40% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 88.30% | 0.20% | 0.79% | 10.71% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 3.30% | 0.00% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0141980593 | C -> T | LOC_Os01g72370.1 | upstream_gene_variant ; 2185.0bp to feature; MODIFIER | silent_mutation | Average:52.352; most accessible tissue: Zhenshan97 root, score: 70.636 | N | N | N | N |
| vg0141980593 | C -> T | LOC_Os01g72380.1 | upstream_gene_variant ; 1523.0bp to feature; MODIFIER | silent_mutation | Average:52.352; most accessible tissue: Zhenshan97 root, score: 70.636 | N | N | N | N |
| vg0141980593 | C -> T | LOC_Os01g72370.3 | upstream_gene_variant ; 2185.0bp to feature; MODIFIER | silent_mutation | Average:52.352; most accessible tissue: Zhenshan97 root, score: 70.636 | N | N | N | N |
| vg0141980593 | C -> T | LOC_Os01g72370.2 | upstream_gene_variant ; 2185.0bp to feature; MODIFIER | silent_mutation | Average:52.352; most accessible tissue: Zhenshan97 root, score: 70.636 | N | N | N | N |
| vg0141980593 | C -> T | LOC_Os01g72370-LOC_Os01g72380 | intergenic_region ; MODIFIER | silent_mutation | Average:52.352; most accessible tissue: Zhenshan97 root, score: 70.636 | N | N | N | N |
| vg0141980593 | C -> DEL | N | N | silent_mutation | Average:52.352; most accessible tissue: Zhenshan97 root, score: 70.636 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0141980593 | NA | 7.72E-06 | mr1008 | 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 |
| vg0141980593 | NA | 3.12E-06 | mr1009 | 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 |
| vg0141980593 | 2.99E-06 | 2.99E-06 | mr1770 | 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 |