| Variant ID: vg0517580953 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 17580953 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.56, T: 0.44, others allele: 0.00, population size: 103. )
TTGAAGCTCAGCCGGTCAGATTCACCCTTTATATACCCTTATCTGGAAGATACTCACTCTGTTCCAAAATATAAGAACATACAAACGGATAAGTCATTTC[C/T]
TACTGCTACGGATTTGGACAGGTAGGAAATGTCCCATTTGGTCATTCAGTCTTCGGTTCTTATATTTTTGGACGGAGGTAGTATAAATTTGTCTCAATTT
AAATTGAGACAAATTTATACTACCTCCGTCCAAAAATATAAGAACCGAAGACTGAATGACCAAATGGGACATTTCCTACCTGTCCAAATCCGTAGCAGTA[G/A]
GAAATGACTTATCCGTTTGTATGTTCTTATATTTTGGAACAGAGTGAGTATCTTCCAGATAAGGGTATATAAAGGGTGAATCTGACCGGCTGAGCTTCAA
| 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 | 78.00% | 20.90% | 1.10% | 0.00% | NA |
| All Indica | 2759 | 94.60% | 5.10% | 0.29% | 0.00% | NA |
| All Japonica | 1512 | 48.80% | 48.70% | 2.51% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 75.90% | 22.80% | 1.29% | 0.00% | NA |
| Indica III | 913 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 95.90% | 3.80% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 73.10% | 24.80% | 2.09% | 0.00% | NA |
| Tropical Japonica | 504 | 25.00% | 73.00% | 1.98% | 0.00% | NA |
| Japonica Intermediate | 241 | 21.20% | 73.90% | 4.98% | 0.00% | NA |
| VI/Aromatic | 96 | 11.50% | 87.50% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 64.40% | 30.00% | 5.56% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0517580953 | C -> T | LOC_Os05g30340.1 | upstream_gene_variant ; 306.0bp to feature; MODIFIER | silent_mutation | Average:60.459; most accessible tissue: Callus, score: 94.864 | N | N | N | N |
| vg0517580953 | C -> T | LOC_Os05g30340.2 | upstream_gene_variant ; 1952.0bp to feature; MODIFIER | silent_mutation | Average:60.459; most accessible tissue: Callus, score: 94.864 | N | N | N | N |
| vg0517580953 | C -> T | LOC_Os05g30310.1 | downstream_gene_variant ; 4029.0bp to feature; MODIFIER | silent_mutation | Average:60.459; most accessible tissue: Callus, score: 94.864 | N | N | N | N |
| vg0517580953 | C -> T | LOC_Os05g30320.1 | downstream_gene_variant ; 1787.0bp to feature; MODIFIER | silent_mutation | Average:60.459; most accessible tissue: Callus, score: 94.864 | N | N | N | N |
| vg0517580953 | C -> T | LOC_Os05g30320-LOC_Os05g30340 | intergenic_region ; MODIFIER | silent_mutation | Average:60.459; most accessible tissue: Callus, score: 94.864 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0517580953 | NA | 1.43E-06 | mr1044 | 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 |
| vg0517580953 | NA | 6.35E-06 | mr1415 | 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 |
| vg0517580953 | NA | 9.72E-06 | mr1482 | 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 |
| vg0517580953 | NA | 6.35E-06 | mr1567 | 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 |
| vg0517580953 | NA | 3.66E-06 | mr1002_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 |
| vg0517580953 | NA | 3.06E-07 | mr1167_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 |
| vg0517580953 | NA | 2.49E-08 | mr1408_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 |
| vg0517580953 | NA | 9.39E-08 | mr1554_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 |
| vg0517580953 | NA | 4.83E-06 | mr1562_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 |
| vg0517580953 | 1.58E-06 | 1.58E-06 | mr1581_2 | Jap_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 |
| vg0517580953 | NA | 1.27E-06 | mr1853_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 |
| vg0517580953 | NA | 5.65E-06 | mr1866_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 |