| Variant ID: vg0810521627 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 10521627 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGTCCTTCTGGCTGCATAGCCTGGAAGTGGTCCCACCATAGTGATGCGGGCCCTTGCAGCTGATGGGTTGCGAAGATAACTTTTTCCTCATCATTGCACT[G/A]
GACGGTGTCCAACTTTTTCCCAACGGCATGCAACCAGTCCAAGGCATCAACGGGGTTATTGGAGCTAGAGAAGGTAGGCGGGCGGATGTGGAGGAACTCG
CGAGTTCCTCCACATCCGCCCGCCTACCTTCTCTAGCTCCAATAACCCCGTTGATGCCTTGGACTGGTTGCATGCCGTTGGGAAAAAGTTGGACACCGTC[C/T]
AGTGCAATGATGAGGAAAAAGTTATCTTCGCAACCCATCAGCTGCAAGGGCCCGCATCACTATGGTGGGACCACTTCCAGGCTATGCAGCCAGAAGGACA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 91.50% | 2.70% | 1.18% | 4.61% | NA |
| All Indica | 2759 | 92.10% | 4.40% | 1.67% | 1.85% | NA |
| All Japonica | 1512 | 89.60% | 0.10% | 0.53% | 9.79% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.80% | 0.00% | 1.18% | 1.01% | NA |
| Indica II | 465 | 86.70% | 3.40% | 4.52% | 5.38% | NA |
| Indica III | 913 | 91.10% | 7.10% | 0.77% | 0.99% | NA |
| Indica Intermediate | 786 | 92.10% | 5.10% | 1.40% | 1.40% | NA |
| Temperate Japonica | 767 | 95.30% | 0.00% | 0.39% | 4.30% | NA |
| Tropical Japonica | 504 | 90.70% | 0.00% | 0.20% | 9.13% | NA |
| Japonica Intermediate | 241 | 69.30% | 0.40% | 1.66% | 28.63% | NA |
| VI/Aromatic | 96 | 84.40% | 0.00% | 0.00% | 15.62% | NA |
| Intermediate | 90 | 87.80% | 5.60% | 2.22% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0810521627 | G -> A | LOC_Os08g17170.1 | N | stop_gained | Average:9.591; most accessible tissue: Minghui63 root, score: 19.68 | N | N | N | N |
| vg0810521627 | G -> DEL | LOC_Os08g17170.1 | N | frameshift_variant | Average:9.591; most accessible tissue: Minghui63 root, score: 19.68 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0810521627 | NA | 7.22E-07 | mr1134 | 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 |
| vg0810521627 | NA | 1.71E-08 | mr1134_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 |
| vg0810521627 | 6.25E-06 | 6.24E-06 | mr1670_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 |
| vg0810521627 | 1.36E-07 | 3.90E-10 | mr1672_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 |
| vg0810521627 | NA | 1.92E-08 | mr1769_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 |