| Variant ID: vg0501420891 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 1420891 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 313. )
GGAGTGATGATAAAGCCAGAAATCAGCCTATGCATGCGCTTGACGAATAAGCGGAGGAAACAGCAGCGGCTATCCTTTTCCAAGATGGGCTCCAGGAGAC[G/T]
ATAAGTCATGCCATAGAACTCAATATTTTTTGCCTGGATCAATTGCCAATTGAAAAGGGAGGTGAAAGACAATCAATTGTCCCATCAATAAAGCAAAAGA
TCTTTTGCTTTATTGATGGGACAATTGATTGTCTTTCACCTCCCTTTTCAATTGGCAATTGATCCAGGCAAAAAATATTGAGTTCTATGGCATGACTTAT[C/A]
GTCTCCTGGAGCCCATCTTGGAAAAGGATAGCCGCTGCTGTTTCCTCCGCTTATTCGTCAAGCGCATGCATAGGCTGATTTCTGGCTTTATCATCACTCC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 96.80% | 2.90% | 0.34% | 0.00% | NA |
| All Indica | 2759 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 91.40% | 7.60% | 0.99% | 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 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 77.60% | 19.80% | 2.58% | 0.00% | NA |
| Japonica Intermediate | 241 | 94.60% | 4.60% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 6.70% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0501420891 | G -> T | LOC_Os05g03410.1 | missense_variant ; p.Arg106Ser; MODERATE | nonsynonymous_codon ; R106S | Average:44.923; most accessible tissue: Minghui63 root, score: 69.846 | unknown | unknown | TOLERATED | 0.52 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0501420891 | NA | 5.63E-12 | Grain_width | 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 |
| vg0501420891 | NA | 1.20E-07 | mr1583 | 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 |
| vg0501420891 | NA | 7.93E-08 | mr1696 | 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 |
| vg0501420891 | 4.69E-06 | 2.95E-07 | mr1126_2 | 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 |