| Variant ID: vg0428010105 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 28010105 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GTGAAGAGACAATTGTTTTTGCATGGAGATTTTTTTTTTGTTGGCCATGGACCATTCCACCTATTTGTTACAGTAAGAACCTGTTTATATGGGACTAAAA[C/T]
TTTTAAGTCCCTATCACATCGGATGTTTGGACACTAATTATAAATATTAAACGTAGACTATTAATAAAACCCATCCATAATCTTGGACTAATTCGCGAGA
TCTCGCGAATTAGTCCAAGATTATGGATGGGTTTTATTAATAGTCTACGTTTAATATTTATAATTAGTGTCCAAACATCCGATGTGATAGGGACTTAAAA[G/A]
TTTTAGTCCCATATAAACAGGTTCTTACTGTAACAAATAGGTGGAATGGTCCATGGCCAACAAAAAAAAAATCTCCATGCAAAAACAATTGTCTCTTCAC
| 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 | 86.90% | 8.50% | 1.14% | 3.36% | NA |
| All Indica | 2759 | 94.60% | 3.60% | 0.29% | 1.59% | NA |
| All Japonica | 1512 | 78.00% | 19.40% | 2.51% | 0.00% | NA |
| Aus | 269 | 57.20% | 0.00% | 0.74% | 42.01% | NA |
| Indica I | 595 | 99.50% | 0.30% | 0.17% | 0.00% | NA |
| Indica II | 465 | 98.70% | 0.90% | 0.00% | 0.43% | NA |
| Indica III | 913 | 88.90% | 7.80% | 0.66% | 2.63% | NA |
| Indica Intermediate | 786 | 94.90% | 2.70% | 0.13% | 2.29% | NA |
| Temperate Japonica | 767 | 95.40% | 2.70% | 1.83% | 0.00% | NA |
| Tropical Japonica | 504 | 51.40% | 45.20% | 3.37% | 0.00% | NA |
| Japonica Intermediate | 241 | 78.40% | 18.70% | 2.90% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 77.80% | 13.30% | 6.67% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0428010105 | C -> DEL | N | N | silent_mutation | Average:46.594; most accessible tissue: Zhenshan97 panicle, score: 80.486 | N | N | N | N |
| vg0428010105 | C -> T | LOC_Os04g47170.1 | upstream_gene_variant ; 3614.0bp to feature; MODIFIER | silent_mutation | Average:46.594; most accessible tissue: Zhenshan97 panicle, score: 80.486 | N | N | N | N |
| vg0428010105 | C -> T | LOC_Os04g47160-LOC_Os04g47170 | intergenic_region ; MODIFIER | silent_mutation | Average:46.594; most accessible tissue: Zhenshan97 panicle, score: 80.486 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0428010105 | NA | 2.05E-14 | mr1410 | 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 |
| vg0428010105 | NA | 7.45E-12 | mr1410 | 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 |
| vg0428010105 | NA | 4.78E-06 | mr1078_2 | 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 |
| vg0428010105 | NA | 1.12E-14 | mr1410_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 |
| vg0428010105 | NA | 3.90E-09 | mr1733_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 |