| Variant ID: vg0909595977 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 9595977 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TTCATATCTAATTCATATGAACTCCGAATTGAGCCATTCAACTTGCAAAATTCATCTAAAATTGAGCTCTACATGTTTGTTTAGTTTTTATGTACTTTTT[C/A]
GTTGGTTTTTATTAGAGTTTTTCCTCGTTTTGCGTGCCAGTGTGTAGAATCCGTCGTTTTGAAAGTTCGCGGTCGCAAGGATAAGAGTTCGGAAGATTGT
ACAATCTTCCGAACTCTTATCCTTGCGACCGCGAACTTTCAAAACGACGGATTCTACACACTGGCACGCAAAACGAGGAAAAACTCTAATAAAAACCAAC[G/T]
AAAAAGTACATAAAAACTAAACAAACATGTAGAGCTCAATTTTAGATGAATTTTGCAAGTTGAATGGCTCAATTCGGAGTTCATATGAATTAGATATGAA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 80.80% | 2.80% | 1.27% | 15.17% | NA |
| All Indica | 2759 | 83.60% | 0.10% | 1.01% | 15.33% | NA |
| All Japonica | 1512 | 77.00% | 8.40% | 0.60% | 14.02% | NA |
| Aus | 269 | 79.60% | 0.00% | 0.37% | 20.07% | NA |
| Indica I | 595 | 85.20% | 0.00% | 0.17% | 14.62% | NA |
| Indica II | 465 | 83.20% | 0.00% | 0.22% | 16.56% | NA |
| Indica III | 913 | 82.00% | 0.00% | 2.52% | 15.44% | NA |
| Indica Intermediate | 786 | 84.40% | 0.30% | 0.38% | 15.01% | NA |
| Temperate Japonica | 767 | 77.60% | 6.80% | 0.78% | 14.86% | NA |
| Tropical Japonica | 504 | 76.80% | 11.50% | 0.20% | 11.51% | NA |
| Japonica Intermediate | 241 | 75.50% | 7.10% | 0.83% | 16.60% | NA |
| VI/Aromatic | 96 | 59.40% | 0.00% | 20.83% | 19.79% | NA |
| Intermediate | 90 | 86.70% | 1.10% | 2.22% | 10.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0909595977 | C -> DEL | N | N | silent_mutation | Average:24.678; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| vg0909595977 | C -> A | LOC_Os09g15720.1 | upstream_gene_variant ; 874.0bp to feature; MODIFIER | silent_mutation | Average:24.678; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| vg0909595977 | C -> A | LOC_Os09g15710.1 | downstream_gene_variant ; 4070.0bp to feature; MODIFIER | silent_mutation | Average:24.678; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| vg0909595977 | C -> A | LOC_Os09g15720-LOC_Os09g15740 | intergenic_region ; MODIFIER | silent_mutation | Average:24.678; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0909595977 | 9.42E-09 | NA | Awn_length | 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 |
| vg0909595977 | NA | 3.62E-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 |
| vg0909595977 | 2.19E-08 | NA | mr1549_2 | 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 |