| Variant ID: vg0712512342 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 12512342 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CCCAACGAAACACAGTCGGACTCGAACCTGCCGGTCAGACCGGCCACACACCGCCGGTCTGACCGGCCCTCAACCGGCGGTCTGACCGCCCAACACACGG[T/C]
GGTCAGACCGGCCCACTCGGAGGAAACCAGTAGACTTCCAAACTTTTACAATATTTCCTATTGTAATCCTAGGCGCCAAATTTGGGTGTAAACAGTTACC
GGTAACTGTTTACACCCAAATTTGGCGCCTAGGATTACAATAGGAAATATTGTAAAAGTTTGGAAGTCTACTGGTTTCCTCCGAGTGGGCCGGTCTGACC[A/G]
CCGTGTGTTGGGCGGTCAGACCGCCGGTTGAGGGCCGGTCAGACCGGCGGTGTGTGGCCGGTCTGACCGGCAGGTTCGAGTCCGACTGTGTTTCGTTGGG
| 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 | 65.00% | 25.70% | 0.19% | 9.10% | NA |
| All Indica | 2759 | 95.90% | 2.10% | 0.11% | 1.92% | NA |
| All Japonica | 1512 | 6.30% | 74.30% | 0.26% | 19.05% | NA |
| Aus | 269 | 95.20% | 0.00% | 0.00% | 4.83% | NA |
| Indica I | 595 | 97.30% | 2.70% | 0.00% | 0.00% | NA |
| Indica II | 465 | 96.60% | 3.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.80% | 0.80% | 0.33% | 0.11% | NA |
| Indica Intermediate | 786 | 91.10% | 2.30% | 0.00% | 6.62% | NA |
| Temperate Japonica | 767 | 2.00% | 65.40% | 0.52% | 32.07% | NA |
| Tropical Japonica | 504 | 13.70% | 85.70% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 5.00% | 78.80% | 0.00% | 16.18% | NA |
| VI/Aromatic | 96 | 24.00% | 0.00% | 1.04% | 75.00% | NA |
| Intermediate | 90 | 57.80% | 36.70% | 1.11% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0712512342 | T -> DEL | N | N | silent_mutation | Average:56.051; most accessible tissue: Zhenshan97 flag leaf, score: 76.356 | N | N | N | N |
| vg0712512342 | T -> C | LOC_Os07g22310.1 | upstream_gene_variant ; 624.0bp to feature; MODIFIER | silent_mutation | Average:56.051; most accessible tissue: Zhenshan97 flag leaf, score: 76.356 | N | N | N | N |
| vg0712512342 | T -> C | LOC_Os07g22320.1 | downstream_gene_variant ; 822.0bp to feature; MODIFIER | silent_mutation | Average:56.051; most accessible tissue: Zhenshan97 flag leaf, score: 76.356 | N | N | N | N |
| vg0712512342 | T -> C | LOC_Os07g22310-LOC_Os07g22320 | intergenic_region ; MODIFIER | silent_mutation | Average:56.051; most accessible tissue: Zhenshan97 flag leaf, score: 76.356 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0712512342 | NA | 5.53E-13 | mr1035 | 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 |
| vg0712512342 | NA | 4.72E-12 | mr1170 | 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 |
| vg0712512342 | NA | 1.85E-10 | mr1630 | 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 |
| vg0712512342 | 4.45E-06 | NA | mr1835 | 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 |