| Variant ID: vg0317228450 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 17228450 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CACCAAATGCCGGTCACCACCCGATGATTTCCTTCGCCGGAAGAACGCCGTGCGCCACCATCTCTTTCAGATTCTCTTCCGTTACATCGGAGGGAGCCCA[T/C]
TGACTCTCGAAACTTTCTCTCTCTTCCGCCATGGATGCAAGTTGAATGGATTGATTTGGTCCAAGATATGGCTGGAGGGGAGTGAGGAATTGGTGCGGTG
CACCGCACCAATTCCTCACTCCCCTCCAGCCATATCTTGGACCAAATCAATCCATTCAACTTGCATCCATGGCGGAAGAGAGAGAAAGTTTCGAGAGTCA[A/G]
TGGGCTCCCTCCGATGTAACGGAAGAGAATCTGAAAGAGATGGTGGCGCACGGCGTTCTTCCGGCGAAGGAAATCATCGGGTGGTGACCGGCATTTGGTG
| 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 | 39.70% | 0.80% | 2.56% | 56.86% | NA |
| All Indica | 2759 | 9.20% | 1.20% | 3.95% | 85.65% | NA |
| All Japonica | 1512 | 96.20% | 0.00% | 0.07% | 3.70% | NA |
| Aus | 269 | 11.90% | 2.20% | 2.60% | 83.27% | NA |
| Indica I | 595 | 7.10% | 0.80% | 4.03% | 88.07% | NA |
| Indica II | 465 | 13.80% | 2.20% | 1.94% | 82.15% | NA |
| Indica III | 913 | 8.00% | 0.90% | 4.60% | 86.53% | NA |
| Indica Intermediate | 786 | 9.40% | 1.40% | 4.33% | 84.86% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.00% | 0.26% | NA |
| Tropical Japonica | 504 | 89.30% | 0.00% | 0.20% | 10.52% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 88.50% | 0.00% | 1.04% | 10.42% | NA |
| Intermediate | 90 | 58.90% | 0.00% | 3.33% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0317228450 | T -> C | LOC_Os03g30190.1 | synonymous_variant ; p.Gln11Gln; LOW | synonymous_codon | Average:41.514; most accessible tissue: Minghui63 flower, score: 73.172 | N | N | N | N |
| vg0317228450 | T -> DEL | LOC_Os03g30190.1 | N | frameshift_variant | Average:41.514; most accessible tissue: Minghui63 flower, score: 73.172 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0317228450 | NA | 5.32E-07 | mr1215 | 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 |
| vg0317228450 | NA | 3.07E-06 | mr1215 | 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 |
| vg0317228450 | 5.31E-06 | 2.36E-15 | mr1583 | 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 |
| vg0317228450 | 5.46E-07 | 1.08E-08 | mr1583 | 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 |