| Variant ID: vg0609892121 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 9892121 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ACCCGTCTGGTTGATCCATATAGATCTACTCCTCCAGCTCTCTGTTTAGGAAAGCTGTCTTAACGTCCATCTGATGGATGAGAAGACCATGAGAGGCTGC[T/C]
AGAGCAAGTAGTACTCAAATCGTGGTCAAGCGAGCAACTGGTGAGTATGTGTCGAAAAAATCCTTGCCTTCCTTTTGGGTATAACCCTTGGCCACAAGCC
GGCTTGTGGCCAAGGGTTATACCCAAAAGGAAGGCAAGGATTTTTTCGACACATACTCACCAGTTGCTCGCTTGACCACGATTTGAGTACTACTTGCTCT[A/G]
GCAGCCTCTCATGGTCTTCTCATCCATCAGATGGACGTTAAGACAGCTTTCCTAAACAGAGAGCTGGAGGAGTAGATCTATATGGATCAACCAGACGGGT
| 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 | 73.30% | 12.50% | 6.26% | 7.93% | NA |
| All Indica | 2759 | 73.90% | 5.00% | 9.79% | 11.27% | NA |
| All Japonica | 1512 | 70.20% | 28.40% | 0.93% | 0.46% | NA |
| Aus | 269 | 80.70% | 3.00% | 1.49% | 14.87% | NA |
| Indica I | 595 | 80.50% | 8.70% | 10.59% | 0.17% | NA |
| Indica II | 465 | 69.00% | 5.80% | 12.26% | 12.90% | NA |
| Indica III | 913 | 70.30% | 2.00% | 11.06% | 16.65% | NA |
| Indica Intermediate | 786 | 76.00% | 5.30% | 6.23% | 12.47% | NA |
| Temperate Japonica | 767 | 48.40% | 50.60% | 0.39% | 0.65% | NA |
| Tropical Japonica | 504 | 95.00% | 3.00% | 1.98% | 0.00% | NA |
| Japonica Intermediate | 241 | 87.60% | 11.20% | 0.41% | 0.83% | NA |
| VI/Aromatic | 96 | 89.60% | 0.00% | 2.08% | 8.33% | NA |
| Intermediate | 90 | 68.90% | 14.40% | 6.67% | 10.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0609892121 | T -> C | LOC_Os06g17050.1 | upstream_gene_variant ; 2403.0bp to feature; MODIFIER | silent_mutation | Average:16.202; most accessible tissue: Zhenshan97 root, score: 23.888 | N | N | N | N |
| vg0609892121 | T -> C | LOC_Os06g17060.1 | upstream_gene_variant ; 124.0bp to feature; MODIFIER | silent_mutation | Average:16.202; most accessible tissue: Zhenshan97 root, score: 23.888 | N | N | N | N |
| vg0609892121 | T -> C | LOC_Os06g17070.1 | downstream_gene_variant ; 252.0bp to feature; MODIFIER | silent_mutation | Average:16.202; most accessible tissue: Zhenshan97 root, score: 23.888 | N | N | N | N |
| vg0609892121 | T -> C | LOC_Os06g17060-LOC_Os06g17070 | intergenic_region ; MODIFIER | silent_mutation | Average:16.202; most accessible tissue: Zhenshan97 root, score: 23.888 | N | N | N | N |
| vg0609892121 | T -> DEL | N | N | silent_mutation | Average:16.202; most accessible tissue: Zhenshan97 root, score: 23.888 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0609892121 | NA | 7.08E-08 | mr1977 | 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 |
| vg0609892121 | NA | 2.70E-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 |
| vg0609892121 | NA | 1.34E-10 | mr1977_2 | 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 |