| Variant ID: vg0706618955 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 6618955 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GTTGCTATGACTTCTCTACCGTCCAAGCTACGCGAGTTCCATGCATGCTGAAGATCACTATATCTACACCACCACGTCACTCAAGACAGATGAGGCGGAG[C/T]
GACGAGGGCAGGCGGAGTATAAATAAAGGCTATGTCTCCAACACCGGCGCACGGACCGACGAGGCCGTGGATCGCTGTCGGCGCCCACACACACATCCAC
GTGGATGTGTGTGTGGGCGCCGACAGCGATCCACGGCCTCGTCGGTCCGTGCGCCGGTGTTGGAGACATAGCCTTTATTTATACTCCGCCTGCCCTCGTC[G/A]
CTCCGCCTCATCTGTCTTGAGTGACGTGGTGGTGTAGATATAGTGATCTTCAGCATGCATGGAACTCGCGTAGCTTGGACGGTAGAGAAGTCATAGCAAC
| 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 | 40.00% | 1.50% | 17.99% | 40.46% | NA |
| All Indica | 2759 | 14.40% | 0.00% | 27.73% | 57.85% | NA |
| All Japonica | 1512 | 87.20% | 4.70% | 3.37% | 4.76% | NA |
| Aus | 269 | 10.80% | 0.00% | 7.81% | 81.41% | NA |
| Indica I | 595 | 18.70% | 0.00% | 20.17% | 61.18% | NA |
| Indica II | 465 | 23.40% | 0.00% | 19.14% | 57.42% | NA |
| Indica III | 913 | 3.60% | 0.00% | 38.77% | 57.61% | NA |
| Indica Intermediate | 786 | 18.40% | 0.00% | 25.70% | 55.85% | NA |
| Temperate Japonica | 767 | 77.40% | 8.20% | 5.61% | 8.74% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.40% | 0.40% | NA |
| Japonica Intermediate | 241 | 92.90% | 3.30% | 2.49% | 1.24% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 2.08% | 2.08% | NA |
| Intermediate | 90 | 61.10% | 1.10% | 12.22% | 25.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0706618955 | C -> DEL | N | N | silent_mutation | Average:46.69; most accessible tissue: Minghui63 panicle, score: 64.459 | N | N | N | N |
| vg0706618955 | C -> T | LOC_Os07g11920-LOC_Os07g11970 | intergenic_region ; MODIFIER | silent_mutation | Average:46.69; most accessible tissue: Minghui63 panicle, score: 64.459 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0706618955 | 6.62E-06 | 6.85E-07 | mr1092 | 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 |
| vg0706618955 | 5.97E-06 | 5.97E-06 | mr1750 | 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 |
| vg0706618955 | 8.46E-06 | 5.05E-07 | mr1896 | 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 |
| vg0706618955 | 8.30E-07 | 8.30E-07 | mr1907 | 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 |
| vg0706618955 | 1.13E-07 | 1.13E-07 | mr1935 | 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 |