| Variant ID: vg1020721566 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 20721566 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 113. )
TGGTGATAGGGAACAAATCTGGTCTGCTTACAGAAAACAAAATGGTGGAGAAGAGAGAGGGGGGGGGGTGTCCAGATTGTTTGGCCGAACCGGACATGTC[T/C]
GTGTCTTAACACTGGACTTGCTATATAACATAAGGAAGCAAAATCACACAGACATACATAACCATTTGATTTTACTGGTCCAGGTTGGTTTGCGCTCTCA
TGAGAGCGCAAACCAACCTGGACCAGTAAAATCAAATGGTTATGTATGTCTGTGTGATTTTGCTTCCTTATGTTATATAGCAAGTCCAGTGTTAAGACAC[A/G]
GACATGTCCGGTTCGGCCAAACAATCTGGACACCCCCCCCCCTCTCTCTTCTCCACCATTTTGTTTTCTGTAAGCAGACCAGATTTGTTCCCTATCACCA
| 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 | 36.30% | 4.00% | 0.87% | 58.82% | NA |
| All Indica | 2759 | 3.40% | 0.50% | 1.27% | 94.78% | NA |
| All Japonica | 1512 | 95.40% | 1.10% | 0.26% | 3.17% | NA |
| Aus | 269 | 43.50% | 27.10% | 0.74% | 28.62% | NA |
| Indica I | 595 | 4.70% | 0.00% | 1.68% | 93.61% | NA |
| Indica II | 465 | 2.40% | 0.00% | 1.51% | 96.13% | NA |
| Indica III | 913 | 2.20% | 0.30% | 0.55% | 96.93% | NA |
| Indica Intermediate | 786 | 4.50% | 1.50% | 1.65% | 92.37% | NA |
| Temperate Japonica | 767 | 97.00% | 0.80% | 0.39% | 1.83% | NA |
| Tropical Japonica | 504 | 93.70% | 1.00% | 0.20% | 5.16% | NA |
| Japonica Intermediate | 241 | 94.20% | 2.50% | 0.00% | 3.32% | NA |
| VI/Aromatic | 96 | 20.80% | 75.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 45.60% | 14.40% | 0.00% | 40.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1020721566 | T -> C | LOC_Os10g38900.1 | upstream_gene_variant ; 3485.0bp to feature; MODIFIER | silent_mutation | Average:14.123; most accessible tissue: Callus, score: 86.485 | N | N | N | N |
| vg1020721566 | T -> C | LOC_Os10g38890.1 | intron_variant ; MODIFIER | silent_mutation | Average:14.123; most accessible tissue: Callus, score: 86.485 | N | N | N | N |
| vg1020721566 | T -> DEL | N | N | silent_mutation | Average:14.123; most accessible tissue: Callus, score: 86.485 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1020721566 | NA | 2.07E-09 | Awn_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 |
| vg1020721566 | 1.18E-06 | 1.18E-06 | mr1542 | 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 |
| vg1020721566 | NA | 8.05E-06 | mr1203_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 |
| vg1020721566 | NA | 1.89E-07 | mr1613_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 |
| vg1020721566 | NA | 8.02E-06 | mr1913_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 |
| vg1020721566 | NA | 1.95E-06 | mr1962_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 |