| Variant ID: vg1010540526 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 10540526 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TCTACACAGTGCCACTATTGTTTCTCTGATTTGAGCTAGATTTATTGGCTTTTCTTAATTAGCTTTGTTTCCACGTTTAGAGCCTAAGTACGAGGAAGCT[T/C]
CGGACGCCGCTTTCGAGGGAGAAGACCCGCACCCTGTGCAAGGCAAGCCTCTTTGATCACATTACCCCTATATTTTCAATGATACATTGTTTGCAAAAAT
ATTTTTGCAAACAATGTATCATTGAAAATATAGGGGTAATGTGATCAAAGAGGCTTGCCTTGCACAGGGTGCGGGTCTTCTCCCTCGAAAGCGGCGTCCG[A/G]
AGCTTCCTCGTACTTAGGCTCTAAACGTGGAAACAAAGCTAATTAAGAAAAGCCAATAAATCTAGCTCAAATCAGAGAAACAATAGTGGCACTGTGTAGA
| 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 | 31.40% | 1.20% | 4.08% | 63.31% | NA |
| All Indica | 2759 | 6.20% | 2.00% | 5.29% | 86.48% | NA |
| All Japonica | 1512 | 65.70% | 0.00% | 0.86% | 33.47% | NA |
| Aus | 269 | 72.90% | 0.00% | 6.69% | 20.45% | NA |
| Indica I | 595 | 6.70% | 1.50% | 5.04% | 86.72% | NA |
| Indica II | 465 | 4.90% | 1.50% | 2.58% | 90.97% | NA |
| Indica III | 913 | 5.30% | 2.80% | 6.24% | 85.65% | NA |
| Indica Intermediate | 786 | 7.60% | 1.80% | 5.98% | 84.61% | NA |
| Temperate Japonica | 767 | 80.30% | 0.00% | 0.65% | 19.04% | NA |
| Tropical Japonica | 504 | 49.40% | 0.00% | 0.99% | 49.60% | NA |
| Japonica Intermediate | 241 | 53.10% | 0.00% | 1.24% | 45.64% | NA |
| VI/Aromatic | 96 | 84.40% | 0.00% | 9.38% | 6.25% | NA |
| Intermediate | 90 | 48.90% | 0.00% | 7.78% | 43.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1010540526 | T -> C | LOC_Os10g20780.1 | downstream_gene_variant ; 1582.0bp to feature; MODIFIER | silent_mutation | Average:17.14; most accessible tissue: Callus, score: 94.247 | N | N | N | N |
| vg1010540526 | T -> C | LOC_Os10g20770-LOC_Os10g20780 | intergenic_region ; MODIFIER | silent_mutation | Average:17.14; most accessible tissue: Callus, score: 94.247 | N | N | N | N |
| vg1010540526 | T -> DEL | N | N | silent_mutation | Average:17.14; most accessible tissue: Callus, score: 94.247 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1010540526 | NA | 8.15E-11 | mr1325 | 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 |
| vg1010540526 | NA | 1.31E-12 | mr1326 | 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 |
| vg1010540526 | NA | 1.17E-06 | mr1527 | 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 |
| vg1010540526 | NA | 1.23E-07 | mr1532 | 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 |
| vg1010540526 | NA | 5.52E-11 | mr1553 | 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 |
| vg1010540526 | NA | 2.29E-09 | mr1690 | 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 |