| Variant ID: vg0625461059 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 25461059 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TCAAGTATGGTTTTGTTATTGTTGATGATTTTTCCCGCTTCACTTGGGTGTATTTTCTCCATGACAAGAGTGAGGCTCAAGATGTCTTCAAGCGCTTCGC[T/C]
AAGCAAGCCCAAAACCTCTATGATCTCACCATCAAGAGGGTGCGAAGCGATAATGGAGGAGAATTCAAGAACACTCAAGTGGAGGAATTCCTTGATGAAG
CTTCATCAAGGAATTCCTCCACTTGAGTGTTCTTGAATTCTCCTCCATTATCGCTTCGCACCCTCTTGATGGTGAGATCATAGAGGTTTTGGGCTTGCTT[A/G]
GCGAAGCGCTTGAAGACATCTTGAGCCTCACTCTTGTCATGGAGAAAATACACCCAAGTGAAGCGGGAAAAATCATCAACAATAACAAAACCATACTTGA
| 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 | 23.70% | 2.40% | 33.94% | 39.93% | NA |
| All Indica | 2759 | 3.20% | 2.80% | 33.24% | 60.71% | NA |
| All Japonica | 1512 | 65.20% | 1.00% | 31.48% | 2.31% | NA |
| Aus | 269 | 8.20% | 1.50% | 44.24% | 46.10% | NA |
| Indica I | 595 | 2.90% | 3.40% | 35.46% | 58.32% | NA |
| Indica II | 465 | 3.40% | 4.30% | 33.98% | 58.28% | NA |
| Indica III | 913 | 2.00% | 1.40% | 29.57% | 67.03% | NA |
| Indica Intermediate | 786 | 4.80% | 3.20% | 35.37% | 56.62% | NA |
| Temperate Japonica | 767 | 71.60% | 0.70% | 25.81% | 1.96% | NA |
| Tropical Japonica | 504 | 56.30% | 1.00% | 38.89% | 3.77% | NA |
| Japonica Intermediate | 241 | 63.50% | 2.10% | 34.02% | 0.41% | NA |
| VI/Aromatic | 96 | 5.20% | 14.60% | 64.58% | 15.62% | NA |
| Intermediate | 90 | 20.00% | 4.40% | 33.33% | 42.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0625461059 | T -> C | LOC_Os06g42370.1 | synonymous_variant ; p.Ala633Ala; LOW | synonymous_codon | Average:23.895; most accessible tissue: Callus, score: 33.225 | N | N | N | N |
| vg0625461059 | T -> DEL | LOC_Os06g42370.1 | N | frameshift_variant | Average:23.895; most accessible tissue: Callus, score: 33.225 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0625461059 | NA | 3.45E-07 | mr1227_2 | 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 |
| vg0625461059 | NA | 2.03E-06 | mr1379_2 | Jap_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 |
| vg0625461059 | NA | 1.56E-07 | mr1446_2 | 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 |
| vg0625461059 | 2.31E-06 | NA | mr1793_2 | 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 |