| Variant ID: vg0602179233 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 2179233 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TTGTAAAGAAAATTTTCGCATAAAATATATTATTTTTAGTAGTTTGAAAAACGTGCTAAAAATCAGTATCTTAATTAGAAAAGAACGAGCCCAGGATACA[A/T]
CCAACTTTGCTTTACTGATAATTTACTGAAAACTCCTCTTTTTTTGTGTGTTCTTAATTAATAACAACCAACGGGGTTCACAAAACCGATCAGTTTTCGT
ACGAAAACTGATCGGTTTTGTGAACCCCGTTGGTTGTTATTAATTAAGAACACACAAAAAAAGAGGAGTTTTCAGTAAATTATCAGTAAAGCAAAGTTGG[T/A]
TGTATCCTGGGCTCGTTCTTTTCTAATTAAGATACTGATTTTTAGCACGTTTTTCAAACTACTAAAAATAATATATTTTATGCGAAAATTTTCTTTACAA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 95.90% | 3.60% | 0.51% | 0.00% | NA |
| All Indica | 2759 | 97.80% | 2.00% | 0.22% | 0.00% | NA |
| All Japonica | 1512 | 91.90% | 7.00% | 1.06% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 94.40% | 4.90% | 0.65% | 0.00% | NA |
| Indica III | 913 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 95.90% | 3.80% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 99.60% | 0.10% | 0.26% | 0.00% | NA |
| Tropical Japonica | 504 | 77.80% | 20.00% | 2.18% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.10% | 1.70% | 1.24% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 7.80% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0602179233 | A -> T | LOC_Os06g04940.1 | upstream_gene_variant ; 2307.0bp to feature; MODIFIER | silent_mutation | Average:35.792; most accessible tissue: Minghui63 panicle, score: 75.788 | N | N | N | N |
| vg0602179233 | A -> T | LOC_Os06g04940.2 | upstream_gene_variant ; 2307.0bp to feature; MODIFIER | silent_mutation | Average:35.792; most accessible tissue: Minghui63 panicle, score: 75.788 | N | N | N | N |
| vg0602179233 | A -> T | LOC_Os06g04950.1 | downstream_gene_variant ; 965.0bp to feature; MODIFIER | silent_mutation | Average:35.792; most accessible tissue: Minghui63 panicle, score: 75.788 | N | N | N | N |
| vg0602179233 | A -> T | LOC_Os06g04940-LOC_Os06g04950 | intergenic_region ; MODIFIER | silent_mutation | Average:35.792; most accessible tissue: Minghui63 panicle, score: 75.788 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0602179233 | 6.09E-06 | NA | mr1016 | 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 |
| vg0602179233 | 4.83E-06 | NA | mr1017 | 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 |
| vg0602179233 | 2.76E-06 | NA | mr1055 | 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 |