| Variant ID: vg1108725515 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 8725515 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.83, T: 0.19, others allele: 0.00, population size: 59. )
TGCAACTTGTAGGCTGTTTGGTTGACTGCATGTGTCCCACAGCCAGGCCCAACAAATGCAAAAAGTCCTTCGTAGCCAGGCCAAGCAGGATCGACTGAAT[C/T]
GAGCTTCGCTGCTCGTCCTGGCTCCACGCATGCAGCAGCGCTGCACCCACGCGTGCAAGCGCTGCACCCGCGCATGCGGGGAGAGGCGATGGGGTCCCCA
TGGGGACCCCATCGCCTCTCCCCGCATGCGCGGGTGCAGCGCTTGCACGCGTGGGTGCAGCGCTGCTGCATGCGTGGAGCCAGGACGAGCAGCGAAGCTC[G/A]
ATTCAGTCGATCCTGCTTGGCCTGGCTACGAAGGACTTTTTGCATTTGTTGGGCCTGGCTGTGGGACACATGCAGTCAACCAAACAGCCTACAAGTTGCA
| 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 | 41.30% | 39.50% | 2.98% | 16.17% | NA |
| All Indica | 2759 | 57.60% | 13.00% | 3.84% | 25.59% | NA |
| All Japonica | 1512 | 17.00% | 79.00% | 1.79% | 2.18% | NA |
| Aus | 269 | 26.80% | 69.90% | 0.74% | 2.60% | NA |
| Indica I | 595 | 79.30% | 11.80% | 1.68% | 7.23% | NA |
| Indica II | 465 | 44.10% | 10.80% | 7.31% | 37.85% | NA |
| Indica III | 913 | 54.30% | 13.50% | 1.75% | 30.45% | NA |
| Indica Intermediate | 786 | 52.90% | 14.60% | 5.85% | 26.59% | NA |
| Temperate Japonica | 767 | 3.80% | 94.70% | 1.56% | 0.00% | NA |
| Tropical Japonica | 504 | 39.30% | 56.90% | 1.98% | 1.79% | NA |
| Japonica Intermediate | 241 | 12.40% | 75.50% | 2.07% | 9.96% | NA |
| VI/Aromatic | 96 | 0.00% | 92.70% | 0.00% | 7.29% | NA |
| Intermediate | 90 | 38.90% | 42.20% | 6.67% | 12.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1108725515 | C -> T | LOC_Os11g15400.1 | missense_variant ; p.Arg379Gln; MODERATE | nonsynonymous_codon ; R379Q | Average:39.528; most accessible tissue: Zhenshan97 flag leaf, score: 77.738 | unknown | unknown | DELETERIOUS | 0.00 |
| vg1108725515 | C -> DEL | LOC_Os11g15400.1 | N | frameshift_variant | Average:39.528; most accessible tissue: Zhenshan97 flag leaf, score: 77.738 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1108725515 | NA | 9.95E-10 | mr1093 | 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 |
| vg1108725515 | NA | 8.48E-06 | mr1213 | 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 |
| vg1108725515 | NA | 1.68E-10 | mr1235 | 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 |
| vg1108725515 | NA | 6.05E-12 | mr1243 | 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 |
| vg1108725515 | NA | 1.13E-09 | mr1599 | 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 |
| vg1108725515 | NA | 9.77E-07 | mr1603 | 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 |
| vg1108725515 | NA | 7.58E-12 | mr1784 | 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 |