| Variant ID: vg1205730694 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 5730694 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 117. )
TGACTCTTGGCTAGAACAATCTCAACCACTACAATGGATGAACACTAAGCTCAAAGGTGTGTGAGAGAGGTGCAAAGGGTGTACGCAATTGAATTGGGTG[T/C]
GAAAAGAGTCCCCTTGCTGCTGGAGGGGGAGTATTTATACTCCCACCAACCAAAACTAGCCGTTGGGGGCGAAATCCCCCAACTCAGTGCTCTGCCGGTC
GACCGGCAGAGCACTGAGTTGGGGGATTTCGCCCCCAACGGCTAGTTTTGGTTGGTGGGAGTATAAATACTCCCCCTCCAGCAGCAAGGGGACTCTTTTC[A/G]
CACCCAATTCAATTGCGTACACCCTTTGCACCTCTCTCACACACCTTTGAGCTTAGTGTTCATCCATTGTAGTGGTTGAGATTGTTCTAGCCAAGAGTCA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 37.70% | 12.30% | 17.48% | 32.52% | NA |
| All Indica | 2759 | 4.50% | 18.10% | 24.72% | 52.63% | NA |
| All Japonica | 1512 | 93.80% | 0.30% | 3.37% | 2.58% | NA |
| Aus | 269 | 32.70% | 26.00% | 30.11% | 11.15% | NA |
| Indica I | 595 | 2.50% | 2.40% | 16.13% | 78.99% | NA |
| Indica II | 465 | 4.10% | 15.70% | 32.47% | 47.74% | NA |
| Indica III | 913 | 3.50% | 33.40% | 25.08% | 38.01% | NA |
| Indica Intermediate | 786 | 7.50% | 13.70% | 26.21% | 52.54% | NA |
| Temperate Japonica | 767 | 90.00% | 0.50% | 5.35% | 4.17% | NA |
| Tropical Japonica | 504 | 97.40% | 0.00% | 1.59% | 0.99% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 0.83% | 0.83% | NA |
| VI/Aromatic | 96 | 95.80% | 2.10% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 65.60% | 5.60% | 13.33% | 15.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1205730694 | T -> C | LOC_Os12g10690.1 | upstream_gene_variant ; 2025.0bp to feature; MODIFIER | silent_mutation | Average:17.577; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
| vg1205730694 | T -> C | LOC_Os12g10700.1 | upstream_gene_variant ; 1595.0bp to feature; MODIFIER | silent_mutation | Average:17.577; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
| vg1205730694 | T -> C | LOC_Os12g10690-LOC_Os12g10700 | intergenic_region ; MODIFIER | silent_mutation | Average:17.577; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
| vg1205730694 | T -> DEL | N | N | silent_mutation | Average:17.577; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1205730694 | 1.78E-06 | 1.25E-30 | mr1024 | 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 |
| vg1205730694 | NA | 1.63E-11 | mr1281 | 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 |
| vg1205730694 | NA | 5.92E-06 | mr1508 | 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 |
| vg1205730694 | NA | 2.25E-18 | mr1581_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 |