| Variant ID: vg0401895649 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 1895649 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GTAGTCGCGCCTTACGCTCCCAAAAACCTGATCGCCCGCCCGTCCGTGCAAACGTCGCAGCAGCGCGTGGTTTTGGAGGCCTACTCTCCCAATGCGTGTG[C/T]
ACACACTCGTCGGGATGGGATTACCGTAGCAGCAACAGCGTTGGAAAATGGATGAAAGTGTGTCTCACTTTCTCTTTTGGGAGATCAAATCCATTCTCAT
ATGAGAATGGATTTGATCTCCCAAAAGAGAAAGTGAGACACACTTTCATCCATTTTCCAACGCTGTTGCTGCTACGGTAATCCCATCCCGACGAGTGTGT[G/A]
CACACGCATTGGGAGAGTAGGCCTCCAAAACCACGCGCTGCTGCGACGTTTGCACGGACGGGCGGGCGATCAGGTTTTTGGGAGCGTAAGGCGCGACTAC
| 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 | 76.70% | 10.40% | 6.09% | 6.88% | NA |
| All Indica | 2759 | 86.00% | 1.20% | 8.74% | 4.02% | NA |
| All Japonica | 1512 | 58.00% | 25.90% | 2.38% | 13.69% | NA |
| Aus | 269 | 92.20% | 7.10% | 0.00% | 0.74% | NA |
| Indica I | 595 | 77.50% | 0.00% | 16.97% | 5.55% | NA |
| Indica II | 465 | 85.60% | 0.20% | 10.32% | 3.87% | NA |
| Indica III | 913 | 91.60% | 2.40% | 3.07% | 2.96% | NA |
| Indica Intermediate | 786 | 86.30% | 1.40% | 8.14% | 4.20% | NA |
| Temperate Japonica | 767 | 53.70% | 34.70% | 1.43% | 10.17% | NA |
| Tropical Japonica | 504 | 68.10% | 15.90% | 3.37% | 12.70% | NA |
| Japonica Intermediate | 241 | 50.60% | 19.10% | 3.32% | 26.97% | NA |
| VI/Aromatic | 96 | 60.40% | 37.50% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 74.40% | 10.00% | 10.00% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0401895649 | C -> DEL | N | N | silent_mutation | Average:20.47; most accessible tissue: Zhenshan97 flag leaf, score: 28.494 | N | N | N | N |
| vg0401895649 | C -> T | LOC_Os04g04100.1 | downstream_gene_variant ; 744.0bp to feature; MODIFIER | silent_mutation | Average:20.47; most accessible tissue: Zhenshan97 flag leaf, score: 28.494 | N | N | N | N |
| vg0401895649 | C -> T | LOC_Os04g04120.1 | downstream_gene_variant ; 1041.0bp to feature; MODIFIER | silent_mutation | Average:20.47; most accessible tissue: Zhenshan97 flag leaf, score: 28.494 | N | N | N | N |
| vg0401895649 | C -> T | LOC_Os04g04100-LOC_Os04g04120 | intergenic_region ; MODIFIER | silent_mutation | Average:20.47; most accessible tissue: Zhenshan97 flag leaf, score: 28.494 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0401895649 | NA | 7.06E-23 | 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 |
| vg0401895649 | NA | 1.54E-10 | mr1549 | 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 |
| vg0401895649 | NA | 3.94E-08 | mr1624 | 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 |
| vg0401895649 | 3.00E-06 | NA | mr1670 | 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 |
| vg0401895649 | NA | 5.92E-09 | mr1757 | 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 |
| vg0401895649 | NA | 2.55E-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 |