| Variant ID: vg0503927501 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 3927501 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 227. )
GTTAAGTTCCAAATCTTGTCGGGATGAAAGTGCATCGCCATTGCTTCAATTTGATGGACCGATGAAGTTTTAGTCTTCAAAGTCAGGGCATCTGTAAATC[T/C]
GAGAAATGTTGGTTATTTTTCAAGGACAACAGTTCAAAGGTTCTCAGTCAGGCGAAAATAAGACTACCCACTGTAAGGGGGGGGTAGGTCTCTGAGATGA
TCATCTCAGAGACCTACCCCCCCCTTACAGTGGGTAGTCTTATTTTCGCCTGACTGAGAACCTTTGAACTGTTGTCCTTGAAAAATAACCAACATTTCTC[A/G]
GATTTACAGATGCCCTGACTTTGAAGACTAAAACTTCATCGGTCCATCAAATTGAAGCAATGGCGATGCACTTTCATCCCGACAAGATTTGGAACTTAAC
| 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 | 28.30% | 8.70% | 20.23% | 42.74% | NA |
| All Indica | 2759 | 32.70% | 1.20% | 17.36% | 48.79% | NA |
| All Japonica | 1512 | 23.00% | 24.70% | 15.21% | 37.10% | NA |
| Aus | 269 | 17.10% | 0.00% | 52.04% | 30.86% | NA |
| Indica I | 595 | 29.20% | 0.20% | 6.72% | 63.87% | NA |
| Indica II | 465 | 32.30% | 3.20% | 18.92% | 45.59% | NA |
| Indica III | 913 | 39.00% | 0.30% | 20.37% | 40.31% | NA |
| Indica Intermediate | 786 | 28.10% | 1.80% | 20.99% | 49.11% | NA |
| Temperate Japonica | 767 | 19.20% | 41.70% | 15.51% | 23.60% | NA |
| Tropical Japonica | 504 | 22.80% | 3.20% | 14.88% | 59.13% | NA |
| Japonica Intermediate | 241 | 35.70% | 15.40% | 14.94% | 34.02% | NA |
| VI/Aromatic | 96 | 20.80% | 0.00% | 73.96% | 5.21% | NA |
| Intermediate | 90 | 25.60% | 6.70% | 40.00% | 27.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0503927501 | T -> DEL | N | N | silent_mutation | Average:15.59; most accessible tissue: Minghui63 root, score: 19.68 | N | N | N | N |
| vg0503927501 | T -> C | LOC_Os05g07360-LOC_Os05g07380 | intergenic_region ; MODIFIER | silent_mutation | Average:15.59; most accessible tissue: Minghui63 root, score: 19.68 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0503927501 | 7.71E-06 | NA | Grain_thickness | 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 |
| vg0503927501 | 7.13E-07 | 1.57E-21 | Heading_date | 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 |
| vg0503927501 | NA | 1.59E-17 | Heading_date | 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 |
| vg0503927501 | NA | 2.83E-17 | Spikelet_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 |
| vg0503927501 | NA | 6.33E-12 | Spikelet_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 |
| vg0503927501 | NA | 2.54E-07 | mr1354 | 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 |
| vg0503927501 | NA | 4.74E-10 | mr1002_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 |
| vg0503927501 | NA | 4.79E-06 | mr1354_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 |
| vg0503927501 | NA | 1.66E-06 | mr1359_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 |
| vg0503927501 | NA | 4.83E-06 | mr1757_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 |
Address: Room B111, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural university, Wuhan, 430070, China
Comments or Questions? Please contact us. Our website: http://xielab.ncpgr.cn/