| Variant ID: vg0624893517 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 24893517 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.79, A: 0.21, others allele: 0.00, population size: 68. )
AAAATCGTTCTATATTGAGACTGATGCTAAATTTGGTTGCCGACAAATGCCGAGCGGTTAGGAGGTAGTGGGGAGACAACGAAGGTGAGGCAGGACAGGG[G/A]
AGTCTCGTCGCCATGGGAGAACGACAAGACAGAGAAGAAGGTCAGCAAGGTTGCTCGAGAAAGAAGATGATCTGATGGTGGAGATAAAAGTGACTGACAA
TTGTCAGTCACTTTTATCTCCACCATCAGATCATCTTCTTTCTCGAGCAACCTTGCTGACCTTCTTCTCTGTCTTGTCGTTCTCCCATGGCGACGAGACT[C/T]
CCCTGTCCTGCCTCACCTTCGTTGTCTCCCCACTACCTCCTAACCGCTCGGCATTTGTCGGCAACCAAATTTAGCATCAGTCTCAATATAGAACGATTTT
| 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 | 26.40% | 9.50% | 0.32% | 63.73% | NA |
| All Indica | 2759 | 4.00% | 0.70% | 0.47% | 94.93% | NA |
| All Japonica | 1512 | 66.20% | 27.20% | 0.13% | 6.48% | NA |
| Aus | 269 | 8.20% | 1.10% | 0.00% | 90.71% | NA |
| Indica I | 595 | 0.30% | 0.20% | 0.84% | 98.66% | NA |
| Indica II | 465 | 5.40% | 1.70% | 0.00% | 92.90% | NA |
| Indica III | 913 | 1.90% | 0.20% | 0.11% | 97.81% | NA |
| Indica Intermediate | 786 | 8.30% | 0.90% | 0.89% | 89.95% | NA |
| Temperate Japonica | 767 | 52.70% | 43.50% | 0.13% | 3.65% | NA |
| Tropical Japonica | 504 | 81.00% | 5.60% | 0.00% | 13.49% | NA |
| Japonica Intermediate | 241 | 78.40% | 20.30% | 0.41% | 0.83% | NA |
| VI/Aromatic | 96 | 82.30% | 7.30% | 0.00% | 10.42% | NA |
| Intermediate | 90 | 43.30% | 11.10% | 0.00% | 45.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0624893517 | G -> A | LOC_Os06g41510.1 | downstream_gene_variant ; 2406.0bp to feature; MODIFIER | silent_mutation | Average:15.355; most accessible tissue: Callus, score: 92.441 | N | N | N | N |
| vg0624893517 | G -> A | LOC_Os06g41520.1 | downstream_gene_variant ; 759.0bp to feature; MODIFIER | silent_mutation | Average:15.355; most accessible tissue: Callus, score: 92.441 | N | N | N | N |
| vg0624893517 | G -> A | LOC_Os06g41510-LOC_Os06g41520 | intergenic_region ; MODIFIER | silent_mutation | Average:15.355; most accessible tissue: Callus, score: 92.441 | N | N | N | N |
| vg0624893517 | G -> DEL | N | N | silent_mutation | Average:15.355; most accessible tissue: Callus, score: 92.441 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0624893517 | 1.87E-06 | NA | Yield | All | YES | 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 |
| vg0624893517 | NA | 6.28E-06 | Yield | 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 |
| vg0624893517 | NA | 2.68E-08 | mr1449_2 | 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 |
| vg0624893517 | NA | 4.78E-08 | mr1627_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 |