| Variant ID: vg0719951750 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 19951750 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CACTATTGCTTACTAGTCTGTCCCAAAAAAAAGCCAAACCCTGGCTATGAACTTAGACACGCATGTGTCCGGGTTCGTAGCTAGGATTGGACTTTTTTTT[G/A]
GGACGGAGGGGGTATGAGTTAGGAGCATGATGATTGGTAGATTATGTTAAAAAATACTTATATCTTGGTATAAATTTTAAATTTCTAGAATTGCTTATAT
ATATAAGCAATTCTAGAAATTTAAAATTTATACCAAGATATAAGTATTTTTTAACATAATCTACCAATCATCATGCTCCTAACTCATACCCCCTCCGTCC[C/T]
AAAAAAAAGTCCAATCCTAGCTACGAACCCGGACACATGCGTGTCTAAGTTCATAGCCAGGGTTTGGCTTTTTTTTGGGACAGACTAGTAAGCAATAGTG
| 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 | 21.50% | 6.50% | 8.34% | 63.61% | NA |
| All Indica | 2759 | 5.10% | 0.40% | 12.94% | 81.48% | NA |
| All Japonica | 1512 | 54.40% | 19.30% | 1.32% | 24.93% | NA |
| Aus | 269 | 8.60% | 0.00% | 2.97% | 88.48% | NA |
| Indica I | 595 | 2.70% | 0.00% | 13.28% | 84.03% | NA |
| Indica II | 465 | 5.20% | 0.00% | 10.11% | 84.73% | NA |
| Indica III | 913 | 5.80% | 0.80% | 14.68% | 78.75% | NA |
| Indica Intermediate | 786 | 6.20% | 0.60% | 12.34% | 80.79% | NA |
| Temperate Japonica | 767 | 56.70% | 37.40% | 2.35% | 3.52% | NA |
| Tropical Japonica | 504 | 42.90% | 0.20% | 0.40% | 56.55% | NA |
| Japonica Intermediate | 241 | 71.40% | 1.70% | 0.00% | 26.97% | NA |
| VI/Aromatic | 96 | 10.40% | 1.00% | 1.04% | 87.50% | NA |
| Intermediate | 90 | 22.20% | 3.30% | 8.89% | 65.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0719951750 | G -> DEL | N | N | silent_mutation | Average:41.197; most accessible tissue: Callus, score: 71.641 | N | N | N | N |
| vg0719951750 | G -> A | LOC_Os07g33370.1 | upstream_gene_variant ; 695.0bp to feature; MODIFIER | silent_mutation | Average:41.197; most accessible tissue: Callus, score: 71.641 | N | N | N | N |
| vg0719951750 | G -> A | LOC_Os07g33370-LOC_Os07g33380 | intergenic_region ; MODIFIER | silent_mutation | Average:41.197; most accessible tissue: Callus, score: 71.641 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0719951750 | 2.24E-06 | NA | Spikelet_length | 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 |
| vg0719951750 | NA | 3.26E-06 | mr1761_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 |