| Variant ID: vg0601322490 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 1322490 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TTAAGCTGATCCGAGAACGTTTGAAGACAGCACAGAGCCGTCAGAAGAATTACGCTGACAATCGGAGGCGTGACCTTGAGTTCGAAAAAGGAGATCATGT[A/G]
TACCTGCGGGTATCACCCCTCCGTGGTATGAGAAGGTTTGGGATGTCCAGCAAGTTAGCACCCCGCTACATCGGCCCCTACCTCATAACCGCCAGACGTG
CACGTCTGGCGGTTATGAGGTAGGGGCCGATGTAGCGGGGTGCTAACTTGCTGGACATCCCAAACCTTCTCATACCACGGAGGGGTGATACCCGCAGGTA[T/C]
ACATGATCTCCTTTTTCGAACTCAAGGTCACGCCTCCGATTGTCAGCGTAATTCTTCTGACGGCTCTGTGCTGTCTTCAAACGTTCTCGGATCAGCTTAA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 69.40% | 2.20% | 20.44% | 7.89% | NA |
| All Indica | 2759 | 63.40% | 3.60% | 32.73% | 0.25% | NA |
| All Japonica | 1512 | 74.30% | 0.10% | 1.92% | 23.74% | NA |
| Aus | 269 | 88.80% | 1.50% | 9.67% | 0.00% | NA |
| Indica I | 595 | 72.30% | 1.80% | 25.21% | 0.67% | NA |
| Indica II | 465 | 84.10% | 1.90% | 13.98% | 0.00% | NA |
| Indica III | 913 | 43.00% | 5.90% | 50.93% | 0.11% | NA |
| Indica Intermediate | 786 | 68.10% | 3.30% | 28.37% | 0.25% | NA |
| Temperate Japonica | 767 | 86.40% | 0.00% | 0.13% | 13.43% | NA |
| Tropical Japonica | 504 | 53.80% | 0.20% | 5.16% | 40.87% | NA |
| Japonica Intermediate | 241 | 78.40% | 0.00% | 0.83% | 20.75% | NA |
| VI/Aromatic | 96 | 93.80% | 0.00% | 2.08% | 4.17% | NA |
| Intermediate | 90 | 90.00% | 0.00% | 6.67% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0601322490 | A -> G | LOC_Os06g03460.1 | synonymous_variant ; p.Val268Val; LOW | synonymous_codon | Average:19.126; most accessible tissue: Minghui63 young leaf, score: 42.042 | N | N | N | N |
| vg0601322490 | A -> DEL | LOC_Os06g03460.1 | N | frameshift_variant | Average:19.126; most accessible tissue: Minghui63 young leaf, score: 42.042 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0601322490 | 4.00E-07 | 4.00E-07 | mr1267_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 |
| vg0601322490 | 9.39E-06 | 6.82E-06 | mr1655_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 |
| vg0601322490 | NA | 9.83E-06 | mr1669_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 |
| vg0601322490 | NA | 8.90E-06 | mr1682_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 |
| vg0601322490 | 9.47E-06 | 9.47E-06 | mr1738_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 |