| Variant ID: vg0222799001 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 22799001 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GCCCTGCTCAGAACCGTCTGTATTCGTCTTCACAATCCCGTCTTGTGATCCAATCTCAGATATTCAACAGCAAACCGCGTTCGCTATAATCCGATGTGAC[C/T]
AATCTTCCGCCCTCGATGTGCCTCTGCTCTGCACGATCTCGTCGGCCTGGCTTGGTCCACCCATACGCGCGCACTTTGTCACAAGCCTCTGCACAACAAG
CTTGTTGTGCAGAGGCTTGTGACAAAGTGCGCGCGTATGGGTGGACCAAGCCAGGCCGACGAGATCGTGCAGAGCAGAGGCACATCGAGGGCGGAAGATT[G/A]
GTCACATCGGATTATAGCGAACGCGGTTTGCTGTTGAATATCTGAGATTGGATCACAAGACGGGATTGTGAAGACGAATACAGACGGTTCTGAGCAGGGC
| 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 | 56.90% | 6.80% | 14.18% | 22.13% | NA |
| All Indica | 2759 | 37.40% | 9.20% | 20.15% | 33.31% | NA |
| All Japonica | 1512 | 98.10% | 0.10% | 0.20% | 1.59% | NA |
| Aus | 269 | 5.20% | 23.40% | 37.17% | 34.20% | NA |
| Indica I | 595 | 27.40% | 6.40% | 18.99% | 47.23% | NA |
| Indica II | 465 | 38.70% | 14.20% | 12.90% | 34.19% | NA |
| Indica III | 913 | 39.50% | 9.30% | 28.70% | 22.45% | NA |
| Indica Intermediate | 786 | 41.60% | 8.10% | 15.39% | 34.86% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.13% | 0.26% | NA |
| Tropical Japonica | 504 | 95.60% | 0.20% | 0.20% | 3.97% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 0.41% | 0.83% | NA |
| VI/Aromatic | 96 | 90.60% | 2.10% | 6.25% | 1.04% | NA |
| Intermediate | 90 | 80.00% | 3.30% | 5.56% | 11.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0222799001 | C -> T | LOC_Os02g37790.1 | upstream_gene_variant ; 146.0bp to feature; MODIFIER | silent_mutation | Average:10.009; most accessible tissue: Callus, score: 40.029 | N | N | N | N |
| vg0222799001 | C -> T | LOC_Os02g37790-LOC_Os02g37800 | intergenic_region ; MODIFIER | silent_mutation | Average:10.009; most accessible tissue: Callus, score: 40.029 | N | N | N | N |
| vg0222799001 | C -> DEL | N | N | silent_mutation | Average:10.009; most accessible tissue: Callus, score: 40.029 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0222799001 | NA | 1.44E-14 | mr1069 | 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 |
| vg0222799001 | NA | 2.76E-07 | mr1069 | Ind_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 |
| vg0222799001 | NA | 6.26E-06 | mr1072 | Ind_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 |
| vg0222799001 | NA | 1.26E-07 | mr1074 | Ind_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 |
| vg0222799001 | NA | 2.27E-06 | mr1075 | Ind_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 |
| vg0222799001 | NA | 3.38E-06 | mr1077 | Ind_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 |
| vg0222799001 | NA | 9.11E-06 | mr1081 | Ind_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 |
| vg0222799001 | 5.20E-06 | NA | mr1094 | 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 |
| vg0222799001 | 4.90E-06 | NA | mr1094 | 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 |
| vg0222799001 | 6.90E-06 | NA | mr1095 | 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 |
Address: Room B111, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural university, Wuhan, 430070, China
Comments or Questions? Please contact us. Our website: http://xielab.ncpgr.cn/