| Variant ID: vg0518660776 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 18660776 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.52, T: 0.48, others allele: 0.00, population size: 104. )
TTTAGTGTCCGATAAGGACTTTATATTTTCCTTTTATCTTTAGGTTAGTTTCTTTCTTGTCTGACAAGGACTTGTATCAACCCATGGGTATAAATATGTA[T/C]
ACCCGGGGTCTATGTAATCTATCGCTACGATCAATATATTTCGGCGCATCGCCACCCTTTTACCTTTTCTACTTTTGTTTTTTACGTTCCGGCGGAACTT
AAGTTCCGCCGGAACGTAAAAAACAAAAGTAGAAAAGGTAAAAGGGTGGCGATGCGCCGAAATATATTGATCGTAGCGATAGATTACATAGACCCCGGGT[A/G]
TACATATTTATACCCATGGGTTGATACAAGTCCTTGTCAGACAAGAAAGAAACTAACCTAAAGATAAAAGGAAAATATAAAGTCCTTATCGGACACTAAA
| 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 | 36.90% | 35.80% | 21.71% | 5.50% | NA |
| All Indica | 2759 | 54.00% | 3.40% | 34.40% | 8.23% | NA |
| All Japonica | 1512 | 0.70% | 96.60% | 1.39% | 1.32% | NA |
| Aus | 269 | 82.20% | 1.90% | 12.64% | 3.35% | NA |
| Indica I | 595 | 71.40% | 2.90% | 17.98% | 7.73% | NA |
| Indica II | 465 | 43.00% | 4.70% | 42.15% | 10.11% | NA |
| Indica III | 913 | 59.60% | 2.50% | 34.39% | 3.50% | NA |
| Indica Intermediate | 786 | 40.70% | 4.10% | 42.24% | 12.98% | NA |
| Temperate Japonica | 767 | 0.10% | 96.50% | 1.96% | 1.43% | NA |
| Tropical Japonica | 504 | 1.80% | 95.80% | 0.99% | 1.39% | NA |
| Japonica Intermediate | 241 | 0.40% | 98.30% | 0.41% | 0.83% | NA |
| VI/Aromatic | 96 | 3.10% | 95.80% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 24.40% | 47.80% | 23.33% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0518660776 | T -> DEL | N | N | silent_mutation | Average:25.647; most accessible tissue: Zhenshan97 flag leaf, score: 46.427 | N | N | N | N |
| vg0518660776 | T -> C | LOC_Os05g32020.1 | upstream_gene_variant ; 2925.0bp to feature; MODIFIER | silent_mutation | Average:25.647; most accessible tissue: Zhenshan97 flag leaf, score: 46.427 | N | N | N | N |
| vg0518660776 | T -> C | LOC_Os05g32030.1 | upstream_gene_variant ; 2664.0bp to feature; MODIFIER | silent_mutation | Average:25.647; most accessible tissue: Zhenshan97 flag leaf, score: 46.427 | N | N | N | N |
| vg0518660776 | T -> C | LOC_Os05g32010.1 | downstream_gene_variant ; 4176.0bp to feature; MODIFIER | silent_mutation | Average:25.647; most accessible tissue: Zhenshan97 flag leaf, score: 46.427 | N | N | N | N |
| vg0518660776 | T -> C | LOC_Os05g32020-LOC_Os05g32030 | intergenic_region ; MODIFIER | silent_mutation | Average:25.647; most accessible tissue: Zhenshan97 flag leaf, score: 46.427 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0518660776 | 4.61E-06 | NA | mr1973 | 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 |
| vg0518660776 | NA | 6.13E-08 | mr1134_2 | 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 |
| vg0518660776 | NA | 3.62E-08 | mr1600_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 |