| Variant ID: vg0714889859 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 14889859 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TAGTTGTTTCAGAAAATTCCATAGGCCACATATCAACACCAATTGAGCTTTAACTTGGTGGTGTGCCTATTTTCGTGCTCCTGGAAAAGAAAAAAAGAAA[A/G]
GTTGATTTCCACTAGTGCATTAAGCTCACGGCGCGCTCTGTTGAGCTTATCAGCCAGATCAGTTTTGTTGTTTTTGCTGAAACTCGCTGAAGCTTGCCTG
CAGGCAAGCTTCAGCGAGTTTCAGCAAAAACAACAAAACTGATCTGGCTGATAAGCTCAACAGAGCGCGCCGTGAGCTTAATGCACTAGTGGAAATCAAC[T/C]
TTTCTTTTTTTCTTTTCCAGGAGCACGAAAATAGGCACACCACCAAGTTAAAGCTCAATTGGTGTTGATATGTGGCCTATGGAATTTTCTGAAACAACTA
| 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 | 41.80% | 1.80% | 3.11% | 53.24% | NA |
| All Indica | 2759 | 15.50% | 0.00% | 3.30% | 81.15% | NA |
| All Japonica | 1512 | 90.50% | 5.60% | 3.24% | 0.73% | NA |
| Aus | 269 | 16.40% | 0.00% | 1.86% | 81.78% | NA |
| Indica I | 595 | 23.40% | 0.00% | 4.54% | 72.10% | NA |
| Indica II | 465 | 17.80% | 0.00% | 3.44% | 78.71% | NA |
| Indica III | 913 | 3.50% | 0.00% | 1.64% | 94.85% | NA |
| Indica Intermediate | 786 | 22.30% | 0.00% | 4.20% | 73.54% | NA |
| Temperate Japonica | 767 | 86.80% | 6.80% | 5.74% | 0.65% | NA |
| Tropical Japonica | 504 | 98.80% | 0.20% | 0.40% | 0.60% | NA |
| Japonica Intermediate | 241 | 84.60% | 12.90% | 1.24% | 1.24% | NA |
| VI/Aromatic | 96 | 84.40% | 2.10% | 0.00% | 13.54% | NA |
| Intermediate | 90 | 61.10% | 0.00% | 2.22% | 36.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0714889859 | A -> DEL | N | N | silent_mutation | Average:12.294; most accessible tissue: Callus, score: 36.74 | N | N | N | N |
| vg0714889859 | A -> G | LOC_Os07g25950.1 | upstream_gene_variant ; 1010.0bp to feature; MODIFIER | silent_mutation | Average:12.294; most accessible tissue: Callus, score: 36.74 | N | N | N | N |
| vg0714889859 | A -> G | LOC_Os07g25940.1 | downstream_gene_variant ; 2796.0bp to feature; MODIFIER | silent_mutation | Average:12.294; most accessible tissue: Callus, score: 36.74 | N | N | N | N |
| vg0714889859 | A -> G | LOC_Os07g25940-LOC_Os07g25950 | intergenic_region ; MODIFIER | silent_mutation | Average:12.294; most accessible tissue: Callus, score: 36.74 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0714889859 | NA | 1.70E-08 | Awn_length | 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 |
| vg0714889859 | 1.45E-06 | 1.45E-06 | mr1036_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 |
| vg0714889859 | NA | 2.55E-06 | mr1913_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 |