| Variant ID: vg0513935185 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 13935185 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGTCTGTTTCTGTTTATTACGTGGTGCCTTTCCAAACCGAGGCCGAGTGGGATCTCTTCCCTTCCAATCTAGCGGCCGGGACTTGTGAGTCCGACTCCCT[C/T]
CCTCCTGACTCCGTTTCTGTACAGGTGTGTCAAACACAGGTAAAATTTTCTTTTGGTGTCGGATTCAATATTCGTTTGCAAAAACAGAACATGTAGGACG
CGTCCTACATGTTCTGTTTTTGCAAACGAATATTGAATCCGACACCAAAAGAAAATTTTACCTGTGTTTGACACACCTGTACAGAAACGGAGTCAGGAGG[G/A]
AGGGAGTCGGACTCACAAGTCCCGGCCGCTAGATTGGAAGGGAAGAGATCCCACTCGGCCTCGGTTTGGAAAGGCACCACGTAATAAACAGAAACAGACT
| 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 | 52.20% | 2.80% | 1.31% | 43.67% | NA |
| All Indica | 2759 | 58.90% | 0.30% | 0.65% | 40.16% | NA |
| All Japonica | 1512 | 38.20% | 8.00% | 2.71% | 51.12% | NA |
| Aus | 269 | 82.90% | 0.00% | 0.00% | 17.10% | NA |
| Indica I | 595 | 34.50% | 1.00% | 1.85% | 62.69% | NA |
| Indica II | 465 | 67.50% | 0.00% | 0.43% | 32.04% | NA |
| Indica III | 913 | 70.30% | 0.10% | 0.11% | 29.46% | NA |
| Indica Intermediate | 786 | 59.00% | 0.10% | 0.51% | 40.33% | NA |
| Temperate Japonica | 767 | 62.60% | 12.60% | 4.56% | 20.21% | NA |
| Tropical Japonica | 504 | 10.10% | 0.00% | 0.60% | 89.29% | NA |
| Japonica Intermediate | 241 | 19.10% | 10.00% | 1.24% | 69.71% | NA |
| VI/Aromatic | 96 | 4.20% | 1.00% | 0.00% | 94.79% | NA |
| Intermediate | 90 | 43.30% | 2.20% | 3.33% | 51.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0513935185 | C -> T | LOC_Os05g24150.1 | upstream_gene_variant ; 2482.0bp to feature; MODIFIER | silent_mutation | Average:10.651; most accessible tissue: Callus, score: 57.237 | N | N | N | N |
| vg0513935185 | C -> T | LOC_Os05g24160.1 | downstream_gene_variant ; 4508.0bp to feature; MODIFIER | silent_mutation | Average:10.651; most accessible tissue: Callus, score: 57.237 | N | N | N | N |
| vg0513935185 | C -> T | LOC_Os05g24150-LOC_Os05g24160 | intergenic_region ; MODIFIER | silent_mutation | Average:10.651; most accessible tissue: Callus, score: 57.237 | N | N | N | N |
| vg0513935185 | C -> DEL | N | N | silent_mutation | Average:10.651; most accessible tissue: Callus, score: 57.237 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0513935185 | NA | 7.92E-07 | mr1028 | 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 |
| vg0513935185 | NA | 9.93E-07 | mr1648 | 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 |
| vg0513935185 | 2.10E-06 | 2.11E-08 | mr1697 | 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 |
| vg0513935185 | NA | 3.93E-08 | mr1697 | 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 |