| Variant ID: vg0402649523 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 2649523 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GGTCCCAGATTTGCTCCCTGTGCCTCCTTGCGCAGGCGATCTCGAGAAGGGCGATGCCGAAGCTGTACACGTCTGAGCTACGCTTGAACGGGACCTTACC[G/A]
TGTTTCAGACACTGTGGATCAAGGTACCCTTCCGAGCCTATGGCAGTTGTCAGCAACGTTGCATTGTCTTGGTTTGCCATCCTCGATAGGCCAAATTCGG
CCGAATTTGGCCTATCGAGGATGGCAAACCAAGACAATGCAACGTTGCTGACAACTGCCATAGGCTCGGAAGGGTACCTTGATCCACAGTGTCTGAAACA[C/T]
GGTAAGGTCCCGTTCAAGCGTAGCTCAGACGTGTACAGCTTCGGCATCGCCCTTCTCGAGATCGCCTGCGCAAGGAGGCACAGGGAGCAAATCTGGGACC
| 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 | 66.70% | 11.60% | 2.05% | 19.70% | NA |
| All Indica | 2759 | 62.80% | 19.10% | 2.36% | 15.73% | NA |
| All Japonica | 1512 | 67.10% | 0.50% | 1.92% | 30.56% | NA |
| Aus | 269 | 92.90% | 0.40% | 0.00% | 6.69% | NA |
| Indica I | 595 | 94.80% | 0.20% | 0.17% | 4.87% | NA |
| Indica II | 465 | 74.40% | 8.60% | 1.94% | 15.05% | NA |
| Indica III | 913 | 36.10% | 41.70% | 2.41% | 19.72% | NA |
| Indica Intermediate | 786 | 62.80% | 13.20% | 4.20% | 19.72% | NA |
| Temperate Japonica | 767 | 90.00% | 0.00% | 1.30% | 8.74% | NA |
| Tropical Japonica | 504 | 43.10% | 1.20% | 2.38% | 53.37% | NA |
| Japonica Intermediate | 241 | 44.40% | 0.40% | 2.90% | 52.28% | NA |
| VI/Aromatic | 96 | 93.80% | 1.00% | 1.04% | 4.17% | NA |
| Intermediate | 90 | 71.10% | 12.20% | 2.22% | 14.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0402649523 | G -> DEL | LOC_Os04g05330.1 | N | frameshift_variant | Average:31.187; most accessible tissue: Zhenshan97 root, score: 57.64 | N | N | N | N |
| vg0402649523 | G -> A | LOC_Os04g05330.1 | synonymous_variant ; p.His508His; LOW | synonymous_codon | Average:31.187; most accessible tissue: Zhenshan97 root, score: 57.64 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0402649523 | 8.82E-06 | NA | mr1114_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 |
| vg0402649523 | 5.51E-07 | 1.56E-06 | mr1117_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 |
| vg0402649523 | 2.36E-06 | 3.97E-06 | mr1119_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 |
| vg0402649523 | 5.79E-06 | 2.41E-06 | mr1726_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 |