| Variant ID: vg1012944850 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 12944850 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 331. )
GACATCACATTAGCAGCATCTCCAGCAATGACCTGTAGCAACAATTCAAAAGTGAGTTCCACTGGTACCATGGGAAAAAAGCACAGAACCAACTGAAAAA[C/T]
ATACCTTGCATATCCTAATCAATATATCTTCTATAATGCCCCTGGAGGCCTCATCTTCAAGATGTGTTGCTAGAGACTTGAGAGCTGCTTCAGCCACGTG
CACGTGGCTGAAGCAGCTCTCAAGTCTCTAGCAACACATCTTGAAGATGAGGCCTCCAGGGGCATTATAGAAGATATATTGATTAGGATATGCAAGGTAT[G/A]
TTTTTCAGTTGGTTCTGTGCTTTTTTCCCATGGTACCAGTGGAACTCACTTTTGAATTGTTGCTACAGGTCATTGCTGGAGATGCTGCTAATGTGATGTC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 77.50% | 21.60% | 0.85% | 0.00% | NA |
| All Indica | 2759 | 99.50% | 0.40% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 32.60% | 64.90% | 2.51% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.70% | 1.10% | 0.22% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.10% | 0.80% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 40.40% | 55.30% | 4.30% | 0.00% | NA |
| Tropical Japonica | 504 | 18.80% | 81.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 36.50% | 61.40% | 2.07% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 70.00% | 30.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1012944850 | C -> T | LOC_Os10g25110.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:42.858; most accessible tissue: Zhenshan97 young leaf, score: 61.386 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1012944850 | NA | 9.44E-10 | Yield | Jap_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 |
| vg1012944850 | NA | 7.60E-11 | mr1905 | 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 |
| vg1012944850 | NA | 1.62E-11 | mr1705_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 |
| vg1012944850 | NA | 9.57E-08 | mr1765_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 |