| Variant ID: vg0526439140 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 26439140 |
| Reference Allele: G | Alternative Allele: A,T |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CGGGATTGAGGCTGCTGGGGGTGACGACAGGGTCATGGCGAATTTCTTCCCCATGGTCCTAAAAGGTCAGGCGTGGGGTTGGCTGATGAACTTGTCACCC[G/A,T]
CGTCGGTACACTCTTGGGAGGATTTGTGCCAGCAGTTCACCATGAACTTCCAGGGCACATATCCGCGCCCAGGTGAAGAAGCGGACTTGCACGCGGTACA
TGTACCGCGTGCAAGTCCGCTTCTTCACCTGGGCGCGGATATGTGCCCTGGAAGTTCATGGTGAACTGCTGGCACAAATCCTCCCAAGAGTGTACCGACG[C/T,A]
GGGTGACAAGTTCATCAGCCAACCCCACGCCTGACCTTTTAGGACCATGGGGAAGAAATTCGCCATGACCCTGTCGTCACCCCCAGCAGCCTCAATCCCG
| 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 | 53.80% | 5.40% | 36.63% | 4.08% | T: 0.04% |
| All Indica | 2759 | 27.30% | 9.10% | 56.83% | 6.78% | NA |
| All Japonica | 1512 | 94.40% | 0.10% | 5.29% | 0.20% | NA |
| Aus | 269 | 84.80% | 0.40% | 14.87% | 0.00% | NA |
| Indica I | 595 | 4.90% | 10.80% | 77.14% | 7.23% | NA |
| Indica II | 465 | 40.40% | 6.50% | 47.53% | 5.59% | NA |
| Indica III | 913 | 33.20% | 9.40% | 50.60% | 6.79% | NA |
| Indica Intermediate | 786 | 29.50% | 9.20% | 54.20% | 7.12% | NA |
| Temperate Japonica | 767 | 97.30% | 0.10% | 2.22% | 0.39% | NA |
| Tropical Japonica | 504 | 95.80% | 0.20% | 3.97% | 0.00% | NA |
| Japonica Intermediate | 241 | 82.20% | 0.00% | 17.84% | 0.00% | NA |
| VI/Aromatic | 96 | 76.00% | 0.00% | 20.83% | 1.04% | T: 2.08% |
| Intermediate | 90 | 71.10% | 1.10% | 25.56% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0526439140 | G -> T | LOC_Os05g45620.1 | missense_variant ; p.Ala294Ser; MODERATE | nonsynonymous_codon ; A294S | Average:33.894; most accessible tissue: Minghui63 flag leaf, score: 76.453 | unknown | unknown | DELETERIOUS | 0.00 |
| vg0526439140 | G -> DEL | LOC_Os05g45620.1 | N | frameshift_variant | Average:33.894; most accessible tissue: Minghui63 flag leaf, score: 76.453 | N | N | N | N |
| vg0526439140 | G -> A | LOC_Os05g45620.1 | missense_variant ; p.Ala294Thr; MODERATE | nonsynonymous_codon ; A294T | Average:33.894; most accessible tissue: Minghui63 flag leaf, score: 76.453 | unknown | unknown | DELETERIOUS | 0.02 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0526439140 | NA | 2.79E-09 | mr1193_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 |
| vg0526439140 | NA | 4.84E-12 | mr1349_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 |
| vg0526439140 | NA | 6.71E-07 | mr1896_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 |
| vg0526439140 | NA | 7.52E-11 | mr1907_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 |
| vg0526439140 | NA | 2.24E-08 | mr1934_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 |