| Variant ID: vg1213285645 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 13285645 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.90, G: 0.10, others allele: 0.00, population size: 31. )
GGAGAAGATGGCATTCATCACGCCCTTCGGTGTATTCTGCTATGCCAAGGTGCCGTTCGGATTAATAAGCACAGGAAATACCTATCAGCGCGGGATCCAG[A/G]
GAGCACTTGGTGATCAACTTGTACGAAACATCGAGGCCTATGTGGATGACATCGCCGTCAAAACCAAGACGAGCGATTCGCTAATCAACGACCTTAGGGA
TCCCTAAGGTCGTTGATTAGCGAATCGCTCGTCTTGGTTTTGACGGCGATGTCATCCACATAGGCCTCGATGTTTCGTACAAGTTGATCACCAAGTGCTC[T/C]
CTGGATCCCGCGCTGATAGGTATTTCCTGTGCTTATTAATCCGAACGGCACCTTGGCATAGCAGAATACACCGAAGGGCGTGATGAATGCCATCTTCTCC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 36.10% | 16.60% | 1.27% | 46.06% | NA |
| All Indica | 2759 | 41.50% | 3.40% | 1.12% | 54.01% | NA |
| All Japonica | 1512 | 15.80% | 43.90% | 0.79% | 39.48% | NA |
| Aus | 269 | 81.40% | 0.40% | 5.95% | 12.27% | NA |
| Indica I | 595 | 15.60% | 6.10% | 2.35% | 75.97% | NA |
| Indica II | 465 | 53.50% | 4.90% | 0.86% | 40.65% | NA |
| Indica III | 913 | 43.70% | 0.30% | 0.22% | 55.75% | NA |
| Indica Intermediate | 786 | 51.30% | 4.10% | 1.40% | 43.26% | NA |
| Temperate Japonica | 767 | 9.30% | 78.00% | 0.91% | 11.86% | NA |
| Tropical Japonica | 504 | 16.30% | 1.80% | 0.40% | 81.55% | NA |
| Japonica Intermediate | 241 | 35.70% | 23.70% | 1.24% | 39.42% | NA |
| VI/Aromatic | 96 | 70.80% | 0.00% | 0.00% | 29.17% | NA |
| Intermediate | 90 | 40.00% | 26.70% | 1.11% | 32.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1213285645 | A -> DEL | LOC_Os12g23490.1 | N | frameshift_variant | Average:11.28; most accessible tissue: Callus, score: 39.263 | N | N | N | N |
| vg1213285645 | A -> G | LOC_Os12g23490.1 | missense_variant ; p.Arg739Gly; MODERATE | nonsynonymous_codon ; R739G | Average:11.28; most accessible tissue: Callus, score: 39.263 | unknown | unknown | TOLERATED | 1.00 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1213285645 | NA | 1.04E-06 | mr1156 | 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 |
| vg1213285645 | NA | 1.70E-07 | mr1030_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 |
| vg1213285645 | 2.20E-06 | 7.66E-09 | mr1136_2 | Ind_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 |
| vg1213285645 | NA | 2.02E-08 | mr1170_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 |
| vg1213285645 | NA | 3.29E-06 | mr1577_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 |
| vg1213285645 | NA | 4.83E-10 | mr1629_2 | Ind_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 |
| vg1213285645 | NA | 4.96E-06 | mr1780_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 |
| vg1213285645 | NA | 8.07E-09 | mr1792_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 |
| vg1213285645 | NA | 8.87E-07 | mr1965_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 |