| Variant ID: vg0606533311 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 6533311 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.08, others allele: 0.00, population size: 76. )
TGGGTTTTCGTATCCAACTTTGACTGTCCGTCTTATATGAAATTTTTTTATAATTCGTATTTTCATAGTTGTTATCATTATTGTTAGATGATAAAATATG[G/A]
TTAATATTTTATGCGTGACTTGTCTTTTTTATTTTTTTCGTAATTTTTTTAAATAAGACGAATGGTCAAACGTTGGACACGGAAACCAGGGTTTCTCTTT
AAAGAGAAACCCTGGTTTCCGTGTCCAACGTTTGACCATTCGTCTTATTTAAAAAAATTACGAAAAAAATAAAAAAGACAAGTCACGCATAAAATATTAA[C/T]
CATATTTTATCATCTAACAATAATGATAACAACTATGAAAATACGAATTATAAAAAAATTTCATATAAGACGGACAGTCAAAGTTGGATACGAAAACCCA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 54.60% | 32.80% | 0.47% | 12.17% | NA |
| All Indica | 2759 | 38.30% | 40.50% | 0.65% | 20.51% | NA |
| All Japonica | 1512 | 96.00% | 3.60% | 0.13% | 0.26% | NA |
| Aus | 269 | 3.00% | 96.70% | 0.37% | 0.00% | NA |
| Indica I | 595 | 38.70% | 8.10% | 1.18% | 52.10% | NA |
| Indica II | 465 | 61.70% | 32.30% | 0.43% | 5.59% | NA |
| Indica III | 913 | 24.30% | 72.60% | 0.33% | 2.74% | NA |
| Indica Intermediate | 786 | 40.60% | 32.60% | 0.76% | 26.08% | NA |
| Temperate Japonica | 767 | 99.10% | 0.40% | 0.13% | 0.39% | NA |
| Tropical Japonica | 504 | 91.50% | 8.30% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 95.40% | 4.10% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 3.10% | 96.90% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 65.60% | 27.80% | 1.11% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0606533311 | G -> A | LOC_Os06g12190.1 | upstream_gene_variant ; 1435.0bp to feature; MODIFIER | silent_mutation | Average:43.605; most accessible tissue: Callus, score: 72.582 | N | N | N | N |
| vg0606533311 | G -> A | LOC_Os06g12200.1 | downstream_gene_variant ; 4638.0bp to feature; MODIFIER | silent_mutation | Average:43.605; most accessible tissue: Callus, score: 72.582 | N | N | N | N |
| vg0606533311 | G -> A | LOC_Os06g12180-LOC_Os06g12190 | intergenic_region ; MODIFIER | silent_mutation | Average:43.605; most accessible tissue: Callus, score: 72.582 | N | N | N | N |
| vg0606533311 | G -> DEL | N | N | silent_mutation | Average:43.605; most accessible tissue: Callus, score: 72.582 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0606533311 | NA | 2.85E-06 | mr1252 | 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 |
| vg0606533311 | 3.77E-06 | 7.09E-06 | mr1377 | 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 |
| vg0606533311 | 3.51E-06 | 3.50E-06 | mr1377 | 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 |
| vg0606533311 | NA | 1.77E-06 | mr1695 | 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 |