| Variant ID: vg0113605352 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 13605352 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.02, others allele: 0.00, population size: 55. )
CAAGGAATTTATCGCGGCGATTCAAGAATAACTCATGGGATTCATCAACGAACAAATCCTTGATCCCAAGGGTGAATTCTACTACGACAGAAATACAATT[C/G]
ATAGGTCCTTAGCTTCTGAAATAGCGACTACTACTACGTCGAAATCGTAGCTAGCTAGGACATAATGGATTGTAATTAATACATGTCTATTTTTCTATAT
ATATAGAAAAATAGACATGTATTAATTACAATCCATTATGTCCTAGCTAGCTACGATTTCGACGTAGTAGTAGTCGCTATTTCAGAAGCTAAGGACCTAT[G/C]
AATTGTATTTCTGTCGTAGTAGAATTCACCCTTGGGATCAAGGATTTGTTCGTTGATGAATCCCATGAGTTATTCTTGAATCGCCGCGATAAATTCCTTG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 53.00% | 8.40% | 9.59% | 28.99% | NA |
| All Indica | 2759 | 36.50% | 14.10% | 13.81% | 35.59% | NA |
| All Japonica | 1512 | 86.60% | 0.00% | 0.40% | 12.96% | NA |
| Aus | 269 | 39.00% | 0.00% | 17.47% | 43.49% | NA |
| Indica I | 595 | 36.50% | 25.40% | 10.08% | 28.07% | NA |
| Indica II | 465 | 29.70% | 4.30% | 15.48% | 50.54% | NA |
| Indica III | 913 | 38.30% | 14.90% | 16.43% | 30.34% | NA |
| Indica Intermediate | 786 | 38.30% | 10.60% | 12.60% | 38.55% | NA |
| Temperate Japonica | 767 | 98.80% | 0.00% | 0.00% | 1.17% | NA |
| Tropical Japonica | 504 | 64.90% | 0.00% | 0.79% | 34.33% | NA |
| Japonica Intermediate | 241 | 93.40% | 0.00% | 0.83% | 5.81% | NA |
| VI/Aromatic | 96 | 30.20% | 1.00% | 9.38% | 59.38% | NA |
| Intermediate | 90 | 60.00% | 8.90% | 11.11% | 20.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0113605352 | C -> G | LOC_Os01g24130.1 | upstream_gene_variant ; 921.0bp to feature; MODIFIER | silent_mutation | Average:8.912; most accessible tissue: Zhenshan97 root, score: 15.132 | N | N | N | N |
| vg0113605352 | C -> G | LOC_Os01g24130-LOC_Os01g24140 | intergenic_region ; MODIFIER | silent_mutation | Average:8.912; most accessible tissue: Zhenshan97 root, score: 15.132 | N | N | N | N |
| vg0113605352 | C -> DEL | N | N | silent_mutation | Average:8.912; most accessible tissue: Zhenshan97 root, score: 15.132 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0113605352 | NA | 5.36E-07 | Awn_length | Ind_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0113605352 | 7.04E-06 | NA | mr1218_2 | 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 |
| vg0113605352 | NA | 5.73E-06 | mr1519_2 | 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 |
| vg0113605352 | 4.50E-06 | NA | mr1871_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 |