| Variant ID: vg1011445819 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 11445819 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.73, A: 0.27, others allele: 0.00, population size: 150. )
TATATGGTACGGGATAAATAATCTCGGCATGCAGGAGTTTTAGGACATCTTTCTTTACAACTTTTCGCATCGCATTATTGAGCCGTCGTTGAGGTTCCCT[A/G]
GAGGGAGTACTCTCAGGATCAATAGGGATACGATGAATACAAAGCGCGGGATTAATCCCTCTGAGATCTTGAAGGGAATAGCCAAGAACAGCGCGATGCT
AGCATCGCGCTGTTCTTGGCTATTCCCTTCAAGATCTCAGAGGGATTAATCCCGCGCTTTGTATTCATCGTATCCCTATTGATCCTGAGAGTACTCCCTC[T/C]
AGGGAACCTCAACGACGGCTCAATAATGCGATGCGAAAAGTTGTAAAGAAAGATGTCCTAAAACTCCTGCATGCCGAGATTATTTATCCCGTACCATATA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 29.00% | 7.60% | 1.31% | 62.04% | NA |
| All Indica | 2759 | 27.70% | 10.70% | 1.88% | 59.70% | NA |
| All Japonica | 1512 | 37.20% | 3.40% | 0.40% | 58.93% | NA |
| Aus | 269 | 1.50% | 0.00% | 0.00% | 98.51% | NA |
| Indica I | 595 | 38.50% | 12.10% | 1.51% | 47.90% | NA |
| Indica II | 465 | 23.90% | 2.40% | 3.23% | 70.54% | NA |
| Indica III | 913 | 24.10% | 16.00% | 1.31% | 58.60% | NA |
| Indica Intermediate | 786 | 26.10% | 8.40% | 2.04% | 63.49% | NA |
| Temperate Japonica | 767 | 68.80% | 6.60% | 0.00% | 24.51% | NA |
| Tropical Japonica | 504 | 3.40% | 0.20% | 0.79% | 95.63% | NA |
| Japonica Intermediate | 241 | 7.50% | 0.00% | 0.83% | 91.70% | NA |
| VI/Aromatic | 96 | 8.30% | 3.10% | 3.12% | 85.42% | NA |
| Intermediate | 90 | 34.40% | 12.20% | 1.11% | 52.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1011445819 | A -> G | LOC_Os10g22160.1 | synonymous_variant ; p.Ser84Ser; LOW | synonymous_codon | Average:18.121; most accessible tissue: Callus, score: 40.51 | N | N | N | N |
| vg1011445819 | A -> DEL | LOC_Os10g22160.1 | N | frameshift_variant | Average:18.121; most accessible tissue: Callus, score: 40.51 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1011445819 | 6.72E-06 | 9.60E-08 | mr1457_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 |
| vg1011445819 | NA | 1.29E-07 | mr1458_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 |