| Variant ID: vg1121675225 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 21675225 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, C: 0.03, others allele: 0.00, population size: 69. )
GCAGGCGAGCAGCATGACGGCGGCGGCGAGGAGGCGGCAGCTGCAGGGATCGGTGCTCGCCGGGAAGATGGTGCTCGTGCGCAAGGCTCTCGACACCAAC[T/C]
TGAACTCCGGCGACGTCGTGTGCCAGCTCGTCAGCTCCACGGTCGGCGACCCCGGTGCGTATCTGGAATCCTCTTTCCTTTTCTCTTAACTAGCATGGTG
CACCATGCTAGTTAAGAGAAAAGGAAAGAGGATTCCAGATACGCACCGGGGTCGCCGACCGTGGAGCTGACGAGCTGGCACACGACGTCGCCGGAGTTCA[A/G]
GTTGGTGTCGAGAGCCTTGCGCACGAGCACCATCTTCCCGGCGAGCACCGATCCCTGCAGCTGCCGCCTCCTCGCCGCCGCCGTCATGCTGCTCGCCTGC
| 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 | 49.60% | 11.70% | 2.35% | 36.31% | NA |
| All Indica | 2759 | 39.10% | 11.90% | 3.12% | 45.96% | NA |
| All Japonica | 1512 | 70.80% | 9.30% | 1.32% | 18.58% | NA |
| Aus | 269 | 54.30% | 24.20% | 0.00% | 21.56% | NA |
| Indica I | 595 | 22.00% | 38.50% | 8.74% | 30.76% | NA |
| Indica II | 465 | 42.40% | 2.20% | 1.94% | 53.55% | NA |
| Indica III | 913 | 44.20% | 3.80% | 1.20% | 50.71% | NA |
| Indica Intermediate | 786 | 44.00% | 6.70% | 1.78% | 47.46% | NA |
| Temperate Japonica | 767 | 82.50% | 7.30% | 0.52% | 9.65% | NA |
| Tropical Japonica | 504 | 55.60% | 13.30% | 3.17% | 27.98% | NA |
| Japonica Intermediate | 241 | 65.10% | 7.50% | 0.00% | 27.39% | NA |
| VI/Aromatic | 96 | 7.30% | 5.20% | 1.04% | 86.46% | NA |
| Intermediate | 90 | 47.80% | 18.90% | 4.44% | 28.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1121675225 | T -> DEL | LOC_Os11g36719.1 | N | frameshift_variant | Average:40.006; most accessible tissue: Minghui63 root, score: 76.721 | N | N | N | N |
| vg1121675225 | T -> C | LOC_Os11g36719.1 | synonymous_variant ; p.Leu38Leu; LOW | synonymous_codon | Average:40.006; most accessible tissue: Minghui63 root, score: 76.721 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1121675225 | NA | 3.74E-07 | mr1014 | 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 |
| vg1121675225 | NA | 1.00E-06 | mr1032 | 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 |
| vg1121675225 | NA | 2.94E-06 | mr1478 | 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 |
| vg1121675225 | NA | 3.98E-06 | mr1479 | 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 |
| vg1121675225 | NA | 3.60E-06 | mr1502 | 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 |
| vg1121675225 | NA | 6.65E-07 | mr1709 | 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 |
| vg1121675225 | NA | 8.87E-07 | mr1709 | 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 |
| vg1121675225 | NA | 1.86E-06 | mr1835 | 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 |
| vg1121675225 | 6.43E-06 | 7.48E-09 | mr1986 | 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 |
| vg1121675225 | 3.80E-06 | 1.85E-07 | mr1986 | 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 |