| Variant ID: vg0612783393 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 12783393 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TATATGATGCTATTTTTTCTATAAATTTGGTCAAACATAAAGAAATTTGTGTCGACGAGTGATACTCGCAGACCGGATGATTAGGGTATCGTGGTACGTT[G/A]
GAACGAGGATCTACGTAATACGACATCAAGCAAACAGACGACAAAGATTATACTGGTTTAGGCCCCTTATTAGGTAATAACCCTAGTCTAGTTTATATGG
CCATATAAACTAGACTAGGGTTATTACCTAATAAGGGGCCTAAACCAGTATAATCTTTGTCGTCTGTTTGCTTGATGTCGTATTACGTAGATCCTCGTTC[C/T]
AACGTACCACGATACCCTAATCATCCGGTCTGCGAGTATCACTCGTCGACACAAATTTCTTTATGTTTGACCAAATTTATAGAAAAAATAGCATCATATA
| 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 | 97.20% | 1.80% | 0.97% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 91.50% | 5.60% | 2.84% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 89.60% | 5.70% | 4.69% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.20% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 81.30% | 16.60% | 2.07% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 0.00% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0612783393 | G -> A | LOC_Os06g22050.1 | upstream_gene_variant ; 450.0bp to feature; MODIFIER | silent_mutation | Average:38.452; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
| vg0612783393 | G -> A | LOC_Os06g22050-LOC_Os06g22060 | intergenic_region ; MODIFIER | silent_mutation | Average:38.452; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0612783393 | NA | 7.46E-06 | Grain_weight | Jap_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0612783393 | 7.41E-06 | 7.41E-06 | mr1141 | 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 |
| vg0612783393 | 3.14E-06 | NA | mr1712 | 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 |