| Variant ID: vg0907725198 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 7725198 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GAAAATGTAATTAATACAATAGTACTTTTTATTTAAGATTCTGTTAGAAAAAAGTAACAGTGACAAAGTTAGCGTAATTATTAGGTTCTTGTGGTGCAAC[C/T]
AGTACAACGGGTTCAAATCCTAGACTTGATACATGTGCTCACATTTACGGCTAATTATTCTTTCAGTGGTACACAACATATCAATCGACAGCAAAAGCTC
GAGCTTTTGCTGTCGATTGATATGTTGTGTACCACTGAAAGAATAATTAGCCGTAAATGTGAGCACATGTATCAAGTCTAGGATTTGAACCCGTTGTACT[G/A]
GTTGCACCACAAGAACCTAATAATTACGCTAACTTTGTCACTGTTACTTTTTTCTAACAGAATCTTAAATAAAAAGTACTATTGTATTAATTACATTTTC
| 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 | 49.10% | 3.50% | 1.33% | 46.09% | NA |
| All Indica | 2759 | 23.20% | 4.00% | 1.34% | 71.40% | NA |
| All Japonica | 1512 | 97.20% | 0.10% | 0.26% | 2.45% | NA |
| Aus | 269 | 20.40% | 18.20% | 7.06% | 54.28% | NA |
| Indica I | 595 | 13.10% | 2.00% | 0.84% | 84.03% | NA |
| Indica II | 465 | 9.90% | 7.30% | 0.65% | 82.15% | NA |
| Indica III | 913 | 37.90% | 3.80% | 1.42% | 56.85% | NA |
| Indica Intermediate | 786 | 21.80% | 3.80% | 2.04% | 72.39% | NA |
| Temperate Japonica | 767 | 95.70% | 0.10% | 0.52% | 3.65% | NA |
| Tropical Japonica | 504 | 99.00% | 0.00% | 0.00% | 0.99% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.40% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 1.04% | 3.12% | NA |
| Intermediate | 90 | 70.00% | 3.30% | 2.22% | 24.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0907725198 | C -> DEL | N | N | silent_mutation | Average:29.068; most accessible tissue: Callus, score: 70.189 | N | N | N | N |
| vg0907725198 | C -> T | LOC_Os09g13380.1 | upstream_gene_variant ; 4421.0bp to feature; MODIFIER | silent_mutation | Average:29.068; most accessible tissue: Callus, score: 70.189 | N | N | N | N |
| vg0907725198 | C -> T | LOC_Os09g13390.1 | downstream_gene_variant ; 1837.0bp to feature; MODIFIER | silent_mutation | Average:29.068; most accessible tissue: Callus, score: 70.189 | N | N | N | N |
| vg0907725198 | C -> T | LOC_Os09g13380-LOC_Os09g13390 | intergenic_region ; MODIFIER | silent_mutation | Average:29.068; most accessible tissue: Callus, score: 70.189 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0907725198 | NA | 5.43E-09 | mr1198 | 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 |
| vg0907725198 | 3.72E-06 | 9.63E-07 | mr1444_2 | 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 |
| vg0907725198 | 3.13E-06 | 3.13E-06 | mr1444_2 | Ind_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 |