| Variant ID: vg1211905124 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 11905124 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.01, others allele: 0.00, population size: 65. )
TATTAGAAGCACTAGAGTGATTTCTCATATTTATTTTGCTGGTACATATTGAACAGCAACAGAGCAATTTCTAACCAAAGAAGTGTAGCTAATGAACTTC[G/A]
ATGTAAGGAGTATCCCTTCAGCAAACTTAAGTAAGAGAGCAGTTTTCAGAACAGGGACTGCTTGCTGCCAACTTGGAGCCAGATTAAGCTGCCCAAGACT
AGTCTTGGGCAGCTTAATCTGGCTCCAAGTTGGCAGCAAGCAGTCCCTGTTCTGAAAACTGCTCTCTTACTTAAGTTTGCTGAAGGGATACTCCTTACAT[C/T]
GAAGTTCATTAGCTACACTTCTTTGGTTAGAAATTGCTCTGTTGCTGTTCAATATGTACCAGCAAAATAAATATGAGAAATCACTCTAGTGCTTCTAATA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 46.70% | 22.70% | 6.83% | 23.68% | NA |
| All Indica | 2759 | 43.90% | 14.40% | 7.50% | 34.22% | NA |
| All Japonica | 1512 | 47.10% | 39.60% | 5.56% | 7.80% | NA |
| Aus | 269 | 59.90% | 21.60% | 7.43% | 11.15% | NA |
| Indica I | 595 | 40.70% | 12.80% | 9.58% | 36.97% | NA |
| Indica II | 465 | 41.50% | 8.80% | 6.02% | 43.66% | NA |
| Indica III | 913 | 47.80% | 17.50% | 6.13% | 28.59% | NA |
| Indica Intermediate | 786 | 43.40% | 15.10% | 8.40% | 33.08% | NA |
| Temperate Japonica | 767 | 83.10% | 4.60% | 4.69% | 7.69% | NA |
| Tropical Japonica | 504 | 5.00% | 90.30% | 2.38% | 2.38% | NA |
| Japonica Intermediate | 241 | 20.70% | 44.80% | 14.94% | 19.50% | NA |
| VI/Aromatic | 96 | 76.00% | 5.20% | 5.21% | 13.54% | NA |
| Intermediate | 90 | 56.70% | 20.00% | 7.78% | 15.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1211905124 | G -> DEL | N | N | silent_mutation | Average:14.709; most accessible tissue: Callus, score: 74.972 | N | N | N | N |
| vg1211905124 | G -> A | LOC_Os12g20390.1 | 3_prime_UTR_variant ; 1372.0bp to feature; MODIFIER | silent_mutation | Average:14.709; most accessible tissue: Callus, score: 74.972 | N | N | N | N |
| vg1211905124 | G -> A | LOC_Os12g20390.4 | 3_prime_UTR_variant ; 1372.0bp to feature; MODIFIER | silent_mutation | Average:14.709; most accessible tissue: Callus, score: 74.972 | N | N | N | N |
| vg1211905124 | G -> A | LOC_Os12g20390.3 | 3_prime_UTR_variant ; 1372.0bp to feature; MODIFIER | silent_mutation | Average:14.709; most accessible tissue: Callus, score: 74.972 | N | N | N | N |
| vg1211905124 | G -> A | LOC_Os12g20380.1 | downstream_gene_variant ; 2538.0bp to feature; MODIFIER | silent_mutation | Average:14.709; most accessible tissue: Callus, score: 74.972 | N | N | N | N |
| vg1211905124 | G -> A | LOC_Os12g20390.2 | downstream_gene_variant ; 1101.0bp to feature; MODIFIER | silent_mutation | Average:14.709; most accessible tissue: Callus, score: 74.972 | N | N | N | N |
| vg1211905124 | G -> A | LOC_Os12g20390.5 | intron_variant ; MODIFIER | silent_mutation | Average:14.709; most accessible tissue: Callus, score: 74.972 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1211905124 | NA | 2.46E-09 | mr1013 | 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 |
| vg1211905124 | NA | 4.40E-07 | mr1031 | 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 |
| vg1211905124 | NA | 5.04E-09 | mr1034 | Jap_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 |
| vg1211905124 | NA | 8.94E-07 | mr1056 | 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 |
| vg1211905124 | NA | 4.23E-06 | mr1171 | 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 |
| vg1211905124 | NA | 1.36E-10 | mr1178 | 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 |
| vg1211905124 | NA | 6.22E-06 | mr1798 | 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 |
| vg1211905124 | NA | 3.34E-07 | mr1870 | 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 |
| vg1211905124 | NA | 1.20E-07 | mr1013_2 | 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 |
| vg1211905124 | NA | 4.10E-06 | mr1425_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 |
| vg1211905124 | NA | 9.42E-06 | mr1803_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 |