| Variant ID: vg0610874578 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr06 | Position: 10874578 |
| Reference Allele: C | Alternative Allele: CGT,T |
| Primary Allele: C | Secondary Allele: CGT |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 78. )
TCCCGGCGTGCTCAGGCCGGCGACGTACGTGAGGCTCGTGGCGAACGTGGCGAGCAGCAGGAGCACCTTGCGCGACTTCTCCTTCACGACGTGCTCGTCG[C/CGT,T]
CGTCGTGCTCGCCGGCGGGCAGCGAGGCGAGCACCACCTGCAGCGCGACGTAGACGACGACGAGGGAGACGAGCACGACGGTGAACGTGGTGGTGGTCCT
AGGACCACCACCACGTTCACCGTCGTGCTCGTCTCCCTCGTCGTCGTCTACGTCGCGCTGCAGGTGGTGCTCGCCTCGCTGCCCGCCGGCGAGCACGACG[G/ACG,A]
CGACGAGCACGTCGTGAAGGAGAAGTCGCGCAAGGTGCTCCTGCTGCTCGCCACGTTCGCCACGAGCCTCACGTACGTCGCCGGCCTGAGCACGCCGGGA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CGT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 67.10% | 31.30% | 0.11% | 0.32% | T: 1.25% |
| All Indica | 2759 | 85.00% | 12.50% | 0.07% | 0.40% | T: 2.03% |
| All Japonica | 1512 | 45.60% | 54.00% | 0.07% | 0.20% | T: 0.13% |
| Aus | 269 | 19.30% | 80.30% | 0.00% | 0.00% | T: 0.37% |
| Indica I | 595 | 95.80% | 3.70% | 0.17% | 0.17% | T: 0.17% |
| Indica II | 465 | 96.60% | 3.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 75.20% | 19.70% | 0.11% | 0.66% | T: 4.27% |
| Indica Intermediate | 786 | 81.30% | 16.20% | 0.00% | 0.51% | T: 2.04% |
| Temperate Japonica | 767 | 70.00% | 30.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 17.50% | 81.70% | 0.00% | 0.40% | T: 0.40% |
| Japonica Intermediate | 241 | 27.00% | 72.20% | 0.41% | 0.41% | NA |
| VI/Aromatic | 96 | 22.90% | 76.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 67.80% | 30.00% | 1.11% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0610874578 | C -> T | LOC_Os06g19110.1 | missense_variant ; p.Gly169Asp; MODERATE | nonsynonymous_codon ; G169D | Average:78.503; most accessible tissue: Zhenshan97 flag leaf, score: 85.638 | unknown | unknown | TOLERATED | 0.48 |
| vg0610874578 | C -> DEL | LOC_Os06g19110.1 | N | frameshift_variant | Average:78.503; most accessible tissue: Zhenshan97 flag leaf, score: 85.638 | N | N | N | N |
| vg0610874578 | C -> CGT | LOC_Os06g19110.1 | frameshift_variant ; p.Gly169fs; HIGH | frameshift_variant | Average:78.503; most accessible tissue: Zhenshan97 flag leaf, score: 85.638 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0610874578 | 3.77E-06 | 3.15E-06 | mr1388 | 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 |
| vg0610874578 | 6.14E-07 | NA | mr1866 | 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 |
| vg0610874578 | 2.51E-08 | 1.77E-09 | mr1866 | 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 |