| Variant ID: vg0607450753 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 7450753 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AATCGGGCAAACGGCCGTCACGGATGAACCTATCTTAATCGGATCCTAATTAAAACCCGTCACTGATAGCTTTGACCCAGACGACATGTCAAACTATAGC[C/T]
CGTCACGAATGACCTATCTCAATCGGACCTAAACTATAGCCCGTCACAGATGACCCTTATCTGTGATGGGCATTAACTATAGCCCGTCACAGATGAGTCA
TGACTCATCTGTGACGGGCTATAGTTAATGCCCATCACAGATAAGGGTCATCTGTGACGGGCTATAGTTTAGGTCCGATTGAGATAGGTCATTCGTGACG[G/A]
GCTATAGTTTGACATGTCGTCTGGGTCAAAGCTATCAGTGACGGGTTTTAATTAGGATCCGATTAAGATAGGTTCATCCGTGACGGCCGTTTGCCCGATT
| 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 | 40.50% | 3.10% | 2.33% | 54.02% | NA |
| All Indica | 2759 | 6.10% | 5.20% | 3.52% | 85.25% | NA |
| All Japonica | 1512 | 98.40% | 0.10% | 0.00% | 1.46% | NA |
| Aus | 269 | 69.50% | 0.00% | 2.60% | 27.88% | NA |
| Indica I | 595 | 5.20% | 2.90% | 3.03% | 88.91% | NA |
| Indica II | 465 | 6.50% | 0.40% | 5.38% | 87.74% | NA |
| Indica III | 913 | 4.20% | 8.70% | 2.19% | 84.99% | NA |
| Indica Intermediate | 786 | 8.70% | 5.70% | 4.33% | 81.30% | NA |
| Temperate Japonica | 767 | 98.80% | 0.00% | 0.00% | 1.17% | NA |
| Tropical Japonica | 504 | 98.80% | 0.40% | 0.00% | 0.79% | NA |
| Japonica Intermediate | 241 | 96.30% | 0.00% | 0.00% | 3.73% | NA |
| VI/Aromatic | 96 | 21.90% | 1.00% | 3.12% | 73.96% | NA |
| Intermediate | 90 | 57.80% | 2.20% | 3.33% | 36.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0607450753 | C -> T | LOC_Os06g13500-LOC_Os06g13510 | intergenic_region ; MODIFIER | silent_mutation | Average:22.632; most accessible tissue: Zhenshan97 panicle, score: 36.038 | N | N | N | N |
| vg0607450753 | C -> DEL | N | N | silent_mutation | Average:22.632; most accessible tissue: Zhenshan97 panicle, score: 36.038 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0607450753 | NA | 7.12E-09 | mr1970 | 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 |
| vg0607450753 | NA | 4.13E-10 | mr1973 | 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 |
| vg0607450753 | NA | 4.05E-09 | mr1970_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 |
| vg0607450753 | 6.58E-07 | NA | mr1973_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 |
| vg0607450753 | 4.80E-07 | 5.77E-15 | mr1973_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 |