| Variant ID: vg0611539416 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 11539416 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CTATATTGTATACTAGAATAGGAAGAGAGTAGAGTAGAAGAAGTCAGAAGAATTCCAGTGTTGTCAGTAATCTTCTCCTATTTTTTTATTCTGTTTATTA[T/C]
TTTGAATTTAATATAATATTCTTCTTGAGTAATTTAGATTTATCTTGTGAGAATTATCTCCTAAATAGCATACGGGATTATTGTTCACTATAATCAACTA
TAGTTGATTATAGTGAACAATAATCCCGTATGCTATTTAGGAGATAATTCTCACAAGATAAATCTAAATTACTCAAGAAGAATATTATATTAAATTCAAA[A/G]
TAATAAACAGAATAAAAAAATAGGAGAAGATTACTGACAACACTGGAATTCTTCTGACTTCTTCTACTCTACTCTCTTCCTATTCTAGTATACAATATAG
| 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 | 34.80% | 8.30% | 3.60% | 53.34% | NA |
| All Indica | 2759 | 5.00% | 9.40% | 4.71% | 80.83% | NA |
| All Japonica | 1512 | 81.70% | 7.90% | 0.20% | 10.12% | NA |
| Aus | 269 | 74.00% | 0.00% | 7.81% | 18.22% | NA |
| Indica I | 595 | 9.20% | 0.20% | 1.51% | 89.08% | NA |
| Indica II | 465 | 3.70% | 0.60% | 1.72% | 93.98% | NA |
| Indica III | 913 | 1.40% | 23.10% | 8.43% | 67.03% | NA |
| Indica Intermediate | 786 | 6.90% | 5.70% | 4.58% | 82.82% | NA |
| Temperate Japonica | 767 | 82.90% | 13.60% | 0.13% | 3.39% | NA |
| Tropical Japonica | 504 | 75.60% | 0.60% | 0.40% | 23.41% | NA |
| Japonica Intermediate | 241 | 90.90% | 5.40% | 0.00% | 3.73% | NA |
| VI/Aromatic | 96 | 32.30% | 7.30% | 9.38% | 51.04% | NA |
| Intermediate | 90 | 43.30% | 4.40% | 7.78% | 44.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0611539416 | T -> C | LOC_Os06g20120.1 | downstream_gene_variant ; 1972.0bp to feature; MODIFIER | silent_mutation | Average:11.378; most accessible tissue: Callus, score: 27.183 | N | N | N | N |
| vg0611539416 | T -> C | LOC_Os06g20120-LOC_Os06g20130 | intergenic_region ; MODIFIER | silent_mutation | Average:11.378; most accessible tissue: Callus, score: 27.183 | N | N | N | N |
| vg0611539416 | T -> DEL | N | N | silent_mutation | Average:11.378; most accessible tissue: Callus, score: 27.183 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0611539416 | 2.49E-06 | NA | Spikelet_length | 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 |
| vg0611539416 | NA | 6.14E-07 | Yield | 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 |
| vg0611539416 | NA | 4.43E-09 | 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 |
| vg0611539416 | NA | 1.41E-07 | 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 |
| vg0611539416 | NA | 5.72E-08 | mr1679_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 |
| vg0611539416 | NA | 8.75E-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 |