| Variant ID: vg0620513547 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 20513547 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CCTACGTCGATGACATTGTTGTCAAGACCAAGACAAGCGACTCATTGATTGACGATCTGCGGGAAACGTTAGACAACCTCCAACGATATCGTCTCATGCT[C/T]
AATCCAGAGAAGTGCACGTTCGGAGTACCATCGGGCAAGCTGCTCGGTTTCCTCGTCTCTGGCAGAGGAATAGAAGCAAATCCCGAGAAGATCAAGGCAA
TTGCCTTGATCTTCTCGGGATTTGCTTCTATTCCTCTGCCAGAGACGAGGAAACCGAGCAGCTTGCCCGATGGTACTCCGAACGTGCACTTCTCTGGATT[G/A]
AGCATGAGACGATATCGTTGGAGGTTGTCTAACGTTTCCCGCAGATCGTCAATCAATGAGTCGCTTGTCTTGGTCTTGACAACAATGTCATCGACGTAGG
| 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 | 76.20% | 1.00% | 8.38% | 14.37% | NA |
| All Indica | 2759 | 70.00% | 0.30% | 7.90% | 21.82% | NA |
| All Japonica | 1512 | 94.60% | 0.10% | 1.19% | 4.17% | NA |
| Aus | 269 | 34.60% | 13.40% | 52.04% | 0.00% | NA |
| Indica I | 595 | 48.60% | 0.00% | 10.08% | 41.34% | NA |
| Indica II | 465 | 76.60% | 0.20% | 5.81% | 17.42% | NA |
| Indica III | 913 | 80.90% | 0.40% | 5.59% | 13.03% | NA |
| Indica Intermediate | 786 | 69.60% | 0.40% | 10.18% | 19.85% | NA |
| Temperate Japonica | 767 | 97.30% | 0.00% | 0.39% | 2.35% | NA |
| Tropical Japonica | 504 | 97.20% | 0.20% | 2.18% | 0.40% | NA |
| Japonica Intermediate | 241 | 80.50% | 0.00% | 1.66% | 17.84% | NA |
| VI/Aromatic | 96 | 74.00% | 2.10% | 18.75% | 5.21% | NA |
| Intermediate | 90 | 85.60% | 2.20% | 2.22% | 10.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0620513547 | C -> T | LOC_Os06g35180.1 | synonymous_variant ; p.Leu269Leu; LOW | synonymous_codon | Average:9.517; most accessible tissue: Callus, score: 34.093 | N | N | N | N |
| vg0620513547 | C -> DEL | LOC_Os06g35180.1 | N | frameshift_variant | Average:9.517; most accessible tissue: Callus, score: 34.093 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0620513547 | NA | 3.33E-06 | mr1060 | 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 |
| vg0620513547 | 4.47E-06 | 8.42E-16 | mr1612 | 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 |
| vg0620513547 | NA | 5.42E-11 | mr1612_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 |