| Variant ID: vg1117516119 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 17516119 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GTTGGCTGCCGAAGCTGTGAGGTGGCGGGGACCGCAGTGGTCCCGGCCGCGGTGATGAGGTGGTGGAGGCGGTGGCCGATGCGTCGGCAACCTTGACTGC[G/A]
AGATGGTGGCGGCCGCGGTATCGAGGTGGTGTCATACCCATGCCTAATGTGTAGTATATCCATGTTGGGTGATGACGAGTGGGCCCATGAAATGGGATGG
CCATCCCATTTCATGGGCCCACTCGTCATCACCCAACATGGATATACTACACATTAGGCATGGGTATGACACCACCTCGATACCGCGGCCGCCACCATCT[C/T]
GCAGTCAAGGTTGCCGACGCATCGGCCACCGCCTCCACCACCTCATCACCGCGGCCGGGACCACTGCGGTCCCCGCCACCTCACAGCTTCGGCAGCCAAC
| 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 | 54.10% | 8.90% | 5.25% | 31.70% | NA |
| All Indica | 2759 | 49.70% | 0.30% | 5.18% | 44.84% | NA |
| All Japonica | 1512 | 54.70% | 26.00% | 4.89% | 14.42% | NA |
| Aus | 269 | 91.10% | 0.40% | 1.49% | 7.06% | NA |
| Indica I | 595 | 31.60% | 0.30% | 7.73% | 60.34% | NA |
| Indica II | 465 | 41.50% | 0.20% | 4.73% | 53.55% | NA |
| Indica III | 913 | 65.10% | 0.10% | 4.27% | 30.56% | NA |
| Indica Intermediate | 786 | 50.30% | 0.60% | 4.58% | 44.53% | NA |
| Temperate Japonica | 767 | 93.70% | 2.60% | 1.69% | 1.96% | NA |
| Tropical Japonica | 504 | 4.80% | 52.80% | 7.14% | 35.32% | NA |
| Japonica Intermediate | 241 | 34.90% | 44.40% | 10.37% | 10.37% | NA |
| VI/Aromatic | 96 | 75.00% | 5.20% | 18.75% | 1.04% | NA |
| Intermediate | 90 | 50.00% | 14.40% | 10.00% | 25.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1117516119 | G -> A | LOC_Os11g30130.1 | upstream_gene_variant ; 470.0bp to feature; MODIFIER | silent_mutation | Average:14.069; most accessible tissue: Callus, score: 53.24 | N | N | N | N |
| vg1117516119 | G -> A | LOC_Os11g30120.1 | downstream_gene_variant ; 2280.0bp to feature; MODIFIER | silent_mutation | Average:14.069; most accessible tissue: Callus, score: 53.24 | N | N | N | N |
| vg1117516119 | G -> A | LOC_Os11g30140.1 | downstream_gene_variant ; 4448.0bp to feature; MODIFIER | silent_mutation | Average:14.069; most accessible tissue: Callus, score: 53.24 | N | N | N | N |
| vg1117516119 | G -> A | LOC_Os11g30120-LOC_Os11g30130 | intergenic_region ; MODIFIER | silent_mutation | Average:14.069; most accessible tissue: Callus, score: 53.24 | N | N | N | N |
| vg1117516119 | G -> DEL | N | N | silent_mutation | Average:14.069; most accessible tissue: Callus, score: 53.24 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1117516119 | NA | 1.44E-07 | mr1401_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 |
| vg1117516119 | NA | 6.73E-09 | mr1509_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 |
| vg1117516119 | NA | 1.84E-06 | mr1582_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 |
| vg1117516119 | NA | 2.18E-06 | mr1730_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 |