| Variant ID: vg0601149832 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 1149832 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 218. )
CCATAAACTCCACATCATCAAGAAACTAGTACTAGACACTACTCTTCCAATGCAAACACCACTATTCCATATTTTAATTTAATGCTACTTATCTCACATG[G/A]
TGTCTTGGATGTTGTGTAGAAACCATGTCTCATGCAAGACATGGTTTCCTTCTCTTTCCTCATTTATTCACTTGCCACATCATTTTTTGTCCTAGGTGGC
GCCACCTAGGACAAAAAATGATGTGGCAAGTGAATAAATGAGGAAAGAGAAGGAAACCATGTCTTGCATGAGACATGGTTTCTACACAACATCCAAGACA[C/T]
CATGTGAGATAAGTAGCATTAAATTAAAATATGGAATAGTGGTGTTTGCATTGGAAGAGTAGTGTCTAGTACTAGTTTCTTGATGATGTGGAGTTTATGG
| 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 | 33.70% | 24.80% | 0.66% | 40.82% | NA |
| All Indica | 2759 | 11.20% | 30.50% | 0.98% | 57.27% | NA |
| All Japonica | 1512 | 79.80% | 14.80% | 0.07% | 5.29% | NA |
| Aus | 269 | 1.90% | 29.40% | 0.37% | 68.40% | NA |
| Indica I | 595 | 3.70% | 21.30% | 1.34% | 73.61% | NA |
| Indica II | 465 | 42.20% | 34.60% | 0.43% | 22.80% | NA |
| Indica III | 913 | 0.90% | 31.40% | 0.77% | 66.92% | NA |
| Indica Intermediate | 786 | 10.70% | 34.00% | 1.27% | 54.07% | NA |
| Temperate Japonica | 767 | 92.60% | 0.10% | 0.00% | 7.30% | NA |
| Tropical Japonica | 504 | 55.60% | 42.50% | 0.00% | 1.98% | NA |
| Japonica Intermediate | 241 | 90.00% | 3.70% | 0.41% | 5.81% | NA |
| VI/Aromatic | 96 | 33.30% | 3.10% | 1.04% | 62.50% | NA |
| Intermediate | 90 | 42.20% | 28.90% | 1.11% | 27.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0601149832 | G -> A | LOC_Os06g03120.1 | upstream_gene_variant ; 3774.0bp to feature; MODIFIER | silent_mutation | Average:29.273; most accessible tissue: Minghui63 panicle, score: 53.77 | N | N | N | N |
| vg0601149832 | G -> A | LOC_Os06g03110.1 | downstream_gene_variant ; 3649.0bp to feature; MODIFIER | silent_mutation | Average:29.273; most accessible tissue: Minghui63 panicle, score: 53.77 | N | N | N | N |
| vg0601149832 | G -> A | LOC_Os06g03110-LOC_Os06g03120 | intergenic_region ; MODIFIER | silent_mutation | Average:29.273; most accessible tissue: Minghui63 panicle, score: 53.77 | N | N | N | N |
| vg0601149832 | G -> DEL | N | N | silent_mutation | Average:29.273; most accessible tissue: Minghui63 panicle, score: 53.77 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0601149832 | NA | 1.55E-06 | mr1377 | 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 |
| vg0601149832 | 3.39E-07 | 3.39E-07 | mr1377 | 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 |
| vg0601149832 | NA | 1.35E-09 | mr1583 | 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 |
| vg0601149832 | NA | 5.58E-07 | mr1870 | 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 |
| vg0601149832 | NA | 1.52E-06 | mr1319_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 |