| Variant ID: vg1208117155 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 8117155 |
| Reference Allele: G | Alternative Allele: C,T |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.62, C: 0.38, others allele: 0.00, population size: 90. )
CCTTCGACAAGATAATGAACTCCCAATGTCCGCATCACCCCAACTCCAACCACGTGGCCAAGGATTGCTTCGTCTACAAACAATTTGCGGAGCAATACGT[G/C,T]
AAGAACGCACGTAAGCCCTCAGACGGAGATCAAGGCACATCAAAGAAGAAAGATGATGAAGACGATGCCCCGACTGGTTTTCAAGATCATCGCAAAGAAC
GTTCTTTGCGATGATCTTGAAAACCAGTCGGGGCATCGTCTTCATCATCTTTCTTCTTTGATGTGCCTTGATCTCCGTCTGAGGGCTTACGTGCGTTCTT[C/G,A]
ACGTATTGCTCCGCAAATTGTTTGTAGACGAAGCAATCCTTGGCCACGTGGTTGGAGTTGGGGTGATGCGGACATTGGGAGTTCATTATCTTGTCGAAGG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 27.50% | 18.90% | 7.60% | 45.92% | T: 0.06% |
| All Indica | 2759 | 33.60% | 6.40% | 11.02% | 48.97% | T: 0.04% |
| All Japonica | 1512 | 4.00% | 43.60% | 1.39% | 50.99% | NA |
| Aus | 269 | 82.90% | 3.30% | 10.78% | 2.23% | T: 0.74% |
| Indica I | 595 | 42.90% | 11.90% | 11.60% | 33.61% | NA |
| Indica II | 465 | 46.00% | 7.10% | 9.25% | 37.63% | NA |
| Indica III | 913 | 22.50% | 1.90% | 11.50% | 64.18% | NA |
| Indica Intermediate | 786 | 32.10% | 7.10% | 11.07% | 49.62% | T: 0.13% |
| Temperate Japonica | 767 | 5.50% | 69.10% | 1.30% | 24.12% | NA |
| Tropical Japonica | 504 | 2.20% | 12.30% | 0.99% | 84.52% | NA |
| Japonica Intermediate | 241 | 3.30% | 27.80% | 2.49% | 66.39% | NA |
| VI/Aromatic | 96 | 71.90% | 18.80% | 2.08% | 7.29% | NA |
| Intermediate | 90 | 22.20% | 35.60% | 3.33% | 38.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1208117155 | G -> C | LOC_Os12g14260.1 | synonymous_variant ; p.Val505Val; LOW | synonymous_codon | Average:15.591; most accessible tissue: Zhenshan97 flower, score: 28.855 | N | N | N | N |
| vg1208117155 | G -> DEL | LOC_Os12g14260.1 | N | frameshift_variant | Average:15.591; most accessible tissue: Zhenshan97 flower, score: 28.855 | N | N | N | N |
| vg1208117155 | G -> T | LOC_Os12g14260.1 | synonymous_variant ; p.Val505Val; LOW | synonymous_codon | Average:15.591; most accessible tissue: Zhenshan97 flower, score: 28.855 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1208117155 | NA | 5.08E-07 | mr1002 | 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 |
| vg1208117155 | 9.18E-07 | 9.18E-07 | mr1153 | 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 |
| vg1208117155 | NA | 1.09E-06 | mr1819 | 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 |
| vg1208117155 | NA | 7.91E-06 | mr1884 | 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 |
| vg1208117155 | NA | 3.27E-06 | mr1884 | 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 |
| vg1208117155 | NA | 4.25E-09 | mr1002_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 |
| vg1208117155 | NA | 6.85E-08 | mr1002_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 |
| vg1208117155 | NA | 4.41E-16 | mr1013_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 |