| Variant ID: vg0606307778 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 6307778 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CATGGAGCAATTAAGCTTAAAAGATTCATCTCGTAATTTACACGTAATCTGTGTAATTAGTTTTTTTTTCTATATTTAATACTCCATATATGTGTCTAAA[T/C]
ATTTGAATTTTTTTTTGAGAGGAGGCCTTCCGTTCCGGCTTATCTTGAAAGCTACATACGGCAGCTAAACATTCGATTTAACAGGGTGAAAAATTTTAAC
GTTAAAATTTTTCACCCTGTTAAATCGAATGTTTAGCTGCCGTATGTAGCTTTCAAGATAAGCCGGAACGGAAGGCCTCCTCTCAAAAAAAAATTCAAAT[A/G]
TTTAGACACATATATGGAGTATTAAATATAGAAAAAAAAACTAATTACACAGATTACGTGTAAATTACGAGATGAATCTTTTAAGCTTAATTGCTCCATG
| 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 | 63.60% | 36.40% | 0.08% | 0.00% | NA |
| All Indica | 2759 | 81.50% | 18.40% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 23.20% | 76.70% | 0.07% | 0.00% | NA |
| Aus | 269 | 96.30% | 3.30% | 0.37% | 0.00% | NA |
| Indica I | 595 | 68.20% | 31.40% | 0.34% | 0.00% | NA |
| Indica II | 465 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Indica III | 913 | 81.30% | 18.70% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 81.80% | 18.20% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 2.10% | 97.80% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 57.30% | 42.70% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 19.10% | 80.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 92.70% | 7.30% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 62.20% | 37.80% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0606307778 | T -> C | LOC_Os06g11860.1 | upstream_gene_variant ; 1117.0bp to feature; MODIFIER | silent_mutation | Average:74.876; most accessible tissue: Zhenshan97 flower, score: 87.172 | N | N | N | N |
| vg0606307778 | T -> C | LOC_Os06g11870.1 | downstream_gene_variant ; 2147.0bp to feature; MODIFIER | silent_mutation | Average:74.876; most accessible tissue: Zhenshan97 flower, score: 87.172 | N | N | N | N |
| vg0606307778 | T -> C | LOC_Os06g11860-LOC_Os06g11870 | intergenic_region ; MODIFIER | silent_mutation | Average:74.876; most accessible tissue: Zhenshan97 flower, score: 87.172 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0606307778 | NA | 5.67E-08 | mr1336_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 |
| vg0606307778 | NA | 5.08E-06 | mr1359_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 |
| vg0606307778 | NA | 2.00E-08 | mr1579_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 |
| vg0606307778 | NA | 1.48E-06 | mr1798_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 |
| vg0606307778 | 7.48E-07 | 7.48E-07 | mr1877_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 |