| Variant ID: vg1116611084 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 16611084 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CAGTCCAAATATCATCGCCATGTAGATATGGGATATCCATAATCTCCACAGTAGCCCCCGAGACCTTTGCAGTCAACCATCATAGCCTTCTCAAAGATAA[C/T]
AATCCGAGTGCTTCAAACTTTTCATGCCAAGGCCTGCCGAGTAGCGAAGACGAAGACTGTAAAGGGCGAAAAGATAAAAAATACGGTGCATCGAATAGAT
ATCTATTCGATGCACCGTATTTTTTATCTTTTCGCCCTTTACAGTCTTCGTCTTCGCTACTCGGCAGGCCTTGGCATGAAAAGTTTGAAGCACTCGGATT[G/A]
TTATCTTTGAGAAGGCTATGATGGTTGACTGCAAAGGTCTCGGGGGCTACTGTGGAGATTATGGATATCCCATATCTACATGGCGATGATATTTGGACTG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 58.90% | 7.10% | 5.50% | 28.48% | NA |
| All Indica | 2759 | 61.70% | 0.40% | 5.65% | 32.29% | NA |
| All Japonica | 1512 | 51.50% | 20.70% | 6.02% | 21.83% | NA |
| Aus | 269 | 57.20% | 1.90% | 2.23% | 38.66% | NA |
| Indica I | 595 | 55.30% | 0.30% | 3.53% | 40.84% | NA |
| Indica II | 465 | 64.30% | 0.00% | 5.16% | 30.54% | NA |
| Indica III | 913 | 61.60% | 0.10% | 7.67% | 30.67% | NA |
| Indica Intermediate | 786 | 65.00% | 1.00% | 5.22% | 28.75% | NA |
| Temperate Japonica | 767 | 85.00% | 3.50% | 2.22% | 9.26% | NA |
| Tropical Japonica | 504 | 11.90% | 38.90% | 11.71% | 37.50% | NA |
| Japonica Intermediate | 241 | 27.40% | 37.30% | 6.22% | 29.05% | NA |
| VI/Aromatic | 96 | 96.90% | 1.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 64.40% | 6.70% | 7.78% | 21.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1116611084 | C -> T | LOC_Os11g28710.1 | upstream_gene_variant ; 647.0bp to feature; MODIFIER | silent_mutation | Average:17.854; most accessible tissue: Zhenshan97 root, score: 27.411 | N | N | N | N |
| vg1116611084 | C -> T | LOC_Os11g28720.1 | upstream_gene_variant ; 974.0bp to feature; MODIFIER | silent_mutation | Average:17.854; most accessible tissue: Zhenshan97 root, score: 27.411 | N | N | N | N |
| vg1116611084 | C -> T | LOC_Os11g28730.1 | downstream_gene_variant ; 4249.0bp to feature; MODIFIER | silent_mutation | Average:17.854; most accessible tissue: Zhenshan97 root, score: 27.411 | N | N | N | N |
| vg1116611084 | C -> T | LOC_Os11g28710-LOC_Os11g28720 | intergenic_region ; MODIFIER | silent_mutation | Average:17.854; most accessible tissue: Zhenshan97 root, score: 27.411 | N | N | N | N |
| vg1116611084 | C -> DEL | N | N | silent_mutation | Average:17.854; most accessible tissue: Zhenshan97 root, score: 27.411 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1116611084 | NA | 4.25E-07 | mr1530 | 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 |
| vg1116611084 | NA | 4.38E-06 | mr1331_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 |
| vg1116611084 | 1.13E-07 | NA | mr1758_2 | 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 |