| Variant ID: vg1008958135 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 8958135 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CTGCAAATGAAACTGGGAGGATTTCGGGGCAACCCGACTCCTCCGTTGAAAGTGTTAAGGCGATCACAACGAGGGGAGGTAAGTCCACTCATGATCCGCC[A/G]
TATCCTAACCCTGCAGGAGCTAATGGGATATCAAAAAAAGCGCCATCTAGTGACTCGGTTGACAAGGAGGTTCAGCTAGAGATAGGGGTGGACGAAAAGC
GCTTTTCGTCCACCCCTATCTCTAGCTGAACCTCCTTGTCAACCGAGTCACTAGATGGCGCTTTTTTTGATATCCCATTAGCTCCTGCAGGGTTAGGATA[T/C]
GGCGGATCATGAGTGGACTTACCTCCCCTCGTTGTGATCGCCTTAACACTTTCAACGGAGGAGTCGGGTTGCCCCGAAATCCTCCCAGTTTCATTTGCAG
| 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 | 22.50% | 0.60% | 7.09% | 69.78% | NA |
| All Indica | 2759 | 5.40% | 0.90% | 11.13% | 82.57% | NA |
| All Japonica | 1512 | 57.90% | 0.20% | 0.60% | 41.34% | NA |
| Aus | 269 | 2.20% | 0.40% | 1.86% | 95.54% | NA |
| Indica I | 595 | 4.40% | 0.50% | 13.45% | 81.68% | NA |
| Indica II | 465 | 3.40% | 0.40% | 13.98% | 82.15% | NA |
| Indica III | 913 | 6.40% | 1.20% | 8.65% | 83.79% | NA |
| Indica Intermediate | 786 | 6.20% | 1.10% | 10.56% | 82.06% | NA |
| Temperate Japonica | 767 | 88.40% | 0.10% | 0.26% | 11.21% | NA |
| Tropical Japonica | 504 | 11.90% | 0.20% | 1.19% | 86.71% | NA |
| Japonica Intermediate | 241 | 56.80% | 0.40% | 0.41% | 42.32% | NA |
| VI/Aromatic | 96 | 8.30% | 0.00% | 8.33% | 83.33% | NA |
| Intermediate | 90 | 28.90% | 0.00% | 6.67% | 64.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1008958135 | A -> G | LOC_Os10g17724.1 | intron_variant ; MODIFIER | silent_mutation | Average:8.424; most accessible tissue: Callus, score: 34.173 | N | N | N | N |
| vg1008958135 | A -> DEL | N | N | silent_mutation | Average:8.424; most accessible tissue: Callus, score: 34.173 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1008958135 | 4.32E-06 | 4.32E-06 | mr1498 | Jap_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 |
| vg1008958135 | NA | 5.96E-09 | mr1709 | 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 |
| vg1008958135 | NA | 1.12E-07 | mr1709 | 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 |
| vg1008958135 | NA | 8.05E-06 | mr1027_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 |
| vg1008958135 | NA | 4.71E-07 | mr1498_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 |