| Variant ID: vg0413193060 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 13193060 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CGATGGTGTGCTGCAGGAGCGGTCCCTCGAACATTGCGACATATTGAGCAAGCACCTCCTCCATCGAAGCGGCGCCGTCACCGCCAGGCAGCCATCCCAT[T/C]
CGCTTGAAGAGGACGCGCTGGCATCGTTCCATCGTCGGCAATGCCGGCTGCTTAGCGATGCGGGCACTCCGACGTTTGGCGCCAGTGTTGTACTGCTTGC
GCAAGCAGTACAACACTGGCGCCAAACGTCGGAGTGCCCGCATCGCTAAGCAGCCGGCATTGCCGACGATGGAACGATGCCAGCGCGTCCTCTTCAAGCG[A/G]
ATGGGATGGCTGCCTGGCGGTGACGGCGCCGCTTCGATGGAGGAGGTGCTTGCTCAATATGTCGCAATGTTCGAGGGACCGCTCCTGCAGCACACCATCG
| 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 | 42.70% | 14.80% | 2.18% | 40.35% | NA |
| All Indica | 2759 | 15.10% | 24.70% | 3.19% | 56.98% | NA |
| All Japonica | 1512 | 96.60% | 0.00% | 0.07% | 3.37% | NA |
| Aus | 269 | 1.90% | 4.10% | 2.97% | 91.08% | NA |
| Indica I | 595 | 26.40% | 5.40% | 2.35% | 65.88% | NA |
| Indica II | 465 | 27.30% | 8.00% | 2.80% | 61.94% | NA |
| Indica III | 913 | 4.60% | 49.30% | 4.49% | 41.62% | NA |
| Indica Intermediate | 786 | 11.60% | 20.70% | 2.54% | 65.14% | NA |
| Temperate Japonica | 767 | 96.70% | 0.00% | 0.13% | 3.13% | NA |
| Tropical Japonica | 504 | 97.80% | 0.00% | 0.00% | 2.18% | NA |
| Japonica Intermediate | 241 | 93.40% | 0.00% | 0.00% | 6.64% | NA |
| VI/Aromatic | 96 | 87.50% | 1.00% | 1.04% | 10.42% | NA |
| Intermediate | 90 | 57.80% | 4.40% | 5.56% | 32.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0413193060 | T -> C | LOC_Os04g23200.1 | synonymous_variant ; p.Arg696Arg; LOW | synonymous_codon | Average:14.378; most accessible tissue: Callus, score: 67.394 | N | N | N | N |
| vg0413193060 | T -> DEL | LOC_Os04g23200.1 | N | frameshift_variant | Average:14.378; most accessible tissue: Callus, score: 67.394 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0413193060 | NA | 8.23E-06 | mr1063 | 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 |
| vg0413193060 | 4.31E-06 | 4.33E-06 | mr1177 | 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 |
| vg0413193060 | NA | 8.74E-06 | mr1177 | 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 |