| Variant ID: vg0623981975 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 23981975 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CAACTCCGATCCATAAGAGACCTTATCGAATGGCAGCCAATGAGTTGGCAGAAGTCAAAAGGCAAGTAGATGATTTGCTTCAGAAAAGATACATCAGACC[A/G]
AGTTCATCACCATGGGGAGCTCCGGTTATTTTTGTGGAAAAGAAAGATCATACCCAGAGGATGTGTGTGGACTATCGTGCCCTAAATGATGTGACTATCA
TGATAGTCACATCATTTAGGGCACGATAGTCCACACACATCCTCTGGGTATGATCTTTCTTTTCCACAAAAATAACCGGAGCTCCCCATGGTGATGAACT[T/C]
GGTCTGATGTATCTTTTCTGAAGCAAATCATCTACTTGCCTTTTGACTTCTGCCAACTCATTGGCTGCCATTCGATAAGGTCTCTTATGGATCGGAGTTG
| 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 | 81.30% | 0.20% | 4.04% | 14.45% | NA |
| All Indica | 2759 | 75.40% | 0.30% | 5.65% | 18.67% | NA |
| All Japonica | 1512 | 88.90% | 0.00% | 1.46% | 9.66% | NA |
| Aus | 269 | 95.90% | 0.40% | 2.97% | 0.74% | NA |
| Indica I | 595 | 52.30% | 0.20% | 8.24% | 39.33% | NA |
| Indica II | 465 | 80.90% | 0.40% | 4.73% | 13.98% | NA |
| Indica III | 913 | 89.50% | 0.10% | 5.81% | 4.60% | NA |
| Indica Intermediate | 786 | 73.40% | 0.40% | 4.07% | 22.14% | NA |
| Temperate Japonica | 767 | 93.10% | 0.00% | 0.78% | 6.13% | NA |
| Tropical Japonica | 504 | 79.80% | 0.00% | 2.78% | 17.46% | NA |
| Japonica Intermediate | 241 | 94.60% | 0.00% | 0.83% | 4.56% | NA |
| VI/Aromatic | 96 | 89.60% | 0.00% | 3.12% | 7.29% | NA |
| Intermediate | 90 | 82.20% | 1.10% | 2.22% | 14.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0623981975 | A -> G | LOC_Os06g40260.1 | synonymous_variant ; p.Pro567Pro; LOW | synonymous_codon | Average:16.999; most accessible tissue: Zhenshan97 root, score: 27.411 | N | N | N | N |
| vg0623981975 | A -> DEL | LOC_Os06g40260.1 | N | frameshift_variant | Average:16.999; most accessible tissue: Zhenshan97 root, score: 27.411 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0623981975 | 3.00E-06 | NA | mr1454_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 |
| vg0623981975 | 5.01E-07 | 5.86E-07 | mr1454_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 |