| Variant ID: vg0417960323 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 17960323 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 49. )
TCACGTGTTGATGATAGCACCGGTCGAGGCAAAGGTAGGGCTGAAGGACTACAAGCGAACAGTGAAGAAGGCTGACGAAAAGTCCAAAAGACAGTCCAAA[G/C]
AAGTCCCTCAGCTTGGAGATCAACCACAGCCCGAGCTGGATCCCGGTGACGCGTTTCTTACACCTAAAAAACGACAGATCAAACTATTCATGAAAGAAAC
GTTTCTTTCATGAATAGTTTGATCTGTCGTTTTTTAGGTGTAAGAAACGCGTCACCGGGATCCAGCTCGGGCTGTGGTTGATCTCCAAGCTGAGGGACTT[C/G]
TTTGGACTGTCTTTTGGACTTTTCGTCAGCCTTCTTCACTGTTCGCTTGTAGTCCTTCAGCCCTACCTTTGCCTCGACCGGTGCTATCATCAACACGTGA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 51.00% | 17.40% | 2.88% | 28.71% | NA |
| All Indica | 2759 | 45.60% | 24.00% | 2.97% | 27.44% | NA |
| All Japonica | 1512 | 51.50% | 8.90% | 2.31% | 37.30% | NA |
| Aus | 269 | 94.10% | 1.50% | 3.35% | 1.12% | NA |
| Indica I | 595 | 89.60% | 1.50% | 1.18% | 7.73% | NA |
| Indica II | 465 | 22.80% | 52.90% | 4.30% | 20.00% | NA |
| Indica III | 913 | 26.10% | 22.50% | 3.29% | 48.19% | NA |
| Indica Intermediate | 786 | 48.50% | 25.70% | 3.18% | 22.65% | NA |
| Temperate Japonica | 767 | 65.40% | 1.80% | 1.43% | 31.29% | NA |
| Tropical Japonica | 504 | 35.70% | 9.90% | 4.37% | 50.00% | NA |
| Japonica Intermediate | 241 | 39.80% | 29.50% | 0.83% | 29.88% | NA |
| VI/Aromatic | 96 | 79.20% | 0.00% | 6.25% | 14.58% | NA |
| Intermediate | 90 | 52.20% | 22.20% | 4.44% | 21.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0417960323 | G -> C | LOC_Os04g30100.1 | missense_variant ; p.Glu162Gln; MODERATE | nonsynonymous_codon ; E162Q | Average:15.404; most accessible tissue: Callus, score: 49.853 | unknown | unknown | TOLERATED | 0.09 |
| vg0417960323 | G -> DEL | LOC_Os04g30100.1 | N | frameshift_variant | Average:15.404; most accessible tissue: Callus, score: 49.853 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0417960323 | NA | 4.79E-06 | mr1064 | 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 |
| vg0417960323 | 3.99E-06 | NA | mr1539 | 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 |
| vg0417960323 | 6.27E-06 | 6.27E-06 | mr1881 | 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 |
| vg0417960323 | NA | 1.69E-06 | mr1745_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 |