| Variant ID: vg0724683198 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 24683198 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 123. )
GAGGAACGCGCTAAGGAATGGATAGGATCGGCCTCGTCGCAAGGATAGGTGTGGAAAAAATTTTCGAGTTCGGCCTGTGACTCTCGCTACCATAGGCACG[C/T]
CCACTGTGGGCTTCGTACCCTAAAACCAGTGTCTCCATTGAATTAAGCCACACATCTAGAGTGTTTGCACTGTGGGATGAGTGTCTCCGGACCAATTTTT
AAAAATTGGTCCGGAGACACTCATCCCACAGTGCAAACACTCTAGATGTGTGGCTTAATTCAATGGAGACACTGGTTTTAGGGTACGAAGCCCACAGTGG[G/A]
CGTGCCTATGGTAGCGAGAGTCACAGGCCGAACTCGAAAATTTTTTCCACACCTATCCTTGCGACGAGGCCGATCCTATCCATTCCTTAGCGCGTTCCTC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 60.90% | 34.60% | 2.71% | 1.78% | NA |
| All Indica | 2759 | 46.70% | 52.40% | 0.36% | 0.51% | NA |
| All Japonica | 1512 | 87.60% | 0.50% | 7.47% | 4.43% | NA |
| Aus | 269 | 51.70% | 48.30% | 0.00% | 0.00% | NA |
| Indica I | 595 | 29.90% | 70.10% | 0.00% | 0.00% | NA |
| Indica II | 465 | 62.80% | 35.30% | 1.08% | 0.86% | NA |
| Indica III | 913 | 50.80% | 48.40% | 0.11% | 0.66% | NA |
| Indica Intermediate | 786 | 45.00% | 53.90% | 0.51% | 0.51% | NA |
| Temperate Japonica | 767 | 97.70% | 0.00% | 2.09% | 0.26% | NA |
| Tropical Japonica | 504 | 78.20% | 0.00% | 12.10% | 9.72% | NA |
| Japonica Intermediate | 241 | 75.50% | 2.90% | 14.94% | 6.64% | NA |
| VI/Aromatic | 96 | 61.50% | 38.50% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 74.40% | 16.70% | 5.56% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0724683198 | C -> DEL | N | N | silent_mutation | Average:69.078; most accessible tissue: Zhenshan97 panicle, score: 88.35 | N | N | N | N |
| vg0724683198 | C -> T | LOC_Os07g41210.1 | upstream_gene_variant ; 324.0bp to feature; MODIFIER | silent_mutation | Average:69.078; most accessible tissue: Zhenshan97 panicle, score: 88.35 | N | N | N | N |
| vg0724683198 | C -> T | LOC_Os07g41220.1 | downstream_gene_variant ; 2672.0bp to feature; MODIFIER | silent_mutation | Average:69.078; most accessible tissue: Zhenshan97 panicle, score: 88.35 | N | N | N | N |
| vg0724683198 | C -> T | LOC_Os07g41210-LOC_Os07g41220 | intergenic_region ; MODIFIER | silent_mutation | Average:69.078; most accessible tissue: Zhenshan97 panicle, score: 88.35 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0724683198 | NA | 5.87E-07 | Spikelet_length | Ind_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 |
| vg0724683198 | NA | 7.49E-08 | mr1088_2 | Ind_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 |
| vg0724683198 | NA | 2.64E-11 | mr1216_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 |
| vg0724683198 | 2.43E-06 | 4.73E-08 | mr1224_2 | Ind_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 |