| Variant ID: vg0619981830 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 19981830 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 117. )
TAGCACCTCCTCTGCCTTCCTCACCCTGAGCGCTAGCGCCCACCTCTCGATCGGCCCGAGCTCTAGGACACAAGATCCAACCTCCTGGTGTAGGGGACAA[C/T]
GGGTTCTGAACGCCCTTATGCTCTCTGCCTCCTCCCCCAAGGTCATCGCTTGCCATCCCTGTCGTCATCTCTTCCCCTCGAGCTCTGGCCGCTATCTCCT
AGGAGATAGCGGCCAGAGCTCGAGGGGAAGAGATGACGACAGGGATGGCAAGCGATGACCTTGGGGGAGGAGGCAGAGAGCATAAGGGCGTTCAGAACCC[G/A]
TTGTCCCCTACACCAGGAGGTTGGATCTTGTGTCCTAGAGCTCGGGCCGATCGAGAGGTGGGCGCTAGCGCTCAGGGTGAGGAAGGCAGAGGAGGTGCTA
| 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 | 38.80% | 32.40% | 12.42% | 16.42% | NA |
| All Indica | 2759 | 51.60% | 4.80% | 18.63% | 24.94% | NA |
| All Japonica | 1512 | 9.60% | 87.40% | 1.85% | 1.19% | NA |
| Aus | 269 | 70.60% | 0.00% | 12.27% | 17.10% | NA |
| Indica I | 595 | 32.90% | 5.00% | 35.63% | 26.39% | NA |
| Indica II | 465 | 48.20% | 5.80% | 23.44% | 22.58% | NA |
| Indica III | 913 | 67.60% | 0.70% | 4.16% | 27.60% | NA |
| Indica Intermediate | 786 | 49.20% | 8.90% | 19.72% | 22.14% | NA |
| Temperate Japonica | 767 | 2.60% | 94.00% | 2.35% | 1.04% | NA |
| Tropical Japonica | 504 | 22.40% | 74.60% | 1.39% | 1.59% | NA |
| Japonica Intermediate | 241 | 5.00% | 92.90% | 1.24% | 0.83% | NA |
| VI/Aromatic | 96 | 46.90% | 35.40% | 6.25% | 11.46% | NA |
| Intermediate | 90 | 31.10% | 47.80% | 6.67% | 14.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0619981830 | C -> T | LOC_Os06g34340.1 | missense_variant ; p.Arg16His; MODERATE | nonsynonymous_codon ; R16H | Average:59.278; most accessible tissue: Minghui63 flag leaf, score: 83.197 | unknown | unknown | DELETERIOUS | 0.00 |
| vg0619981830 | C -> DEL | LOC_Os06g34340.1 | N | frameshift_variant | Average:59.278; most accessible tissue: Minghui63 flag leaf, score: 83.197 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0619981830 | NA | 5.82E-07 | mr1518 | 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 |
| vg0619981830 | NA | 4.85E-09 | mr1676 | 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 |
| vg0619981830 | NA | 5.11E-13 | mr1769 | 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 |
| vg0619981830 | NA | 2.31E-08 | mr1951 | 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 |
| vg0619981830 | NA | 6.80E-06 | mr1398_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 |
| vg0619981830 | NA | 5.76E-12 | mr1676_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 |
| vg0619981830 | NA | 6.59E-15 | mr1769_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 |