| Variant ID: vg0421279302 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 21279302 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TCACAATGTAAGTCATTCTAGCATTTCGCACATTCATATTGATGTTAATGAATTTAGACATATATATTTATCTAGATTCATTAACATCGAGATAAATGTG[G/A]
AAAATATTAGAATGACTTACATTGTGAAACGGAGGAAGTAGTTAACTTCTGGCTACTTTTTAGACAAGCATTTGTCCAGATGCATAGTCAGAACAGAAGT
ACTTCTGTTCTGACTATGCATCTGGACAAATGCTTGTCTAAAAAGTAGCCAGAAGTTAACTACTTCCTCCGTTTCACAATGTAAGTCATTCTAATATTTT[C/T]
CACATTTATCTCGATGTTAATGAATCTAGATAAATATATATGTCTAAATTCATTAACATCAATATGAATGTGCGAAATGCTAGAATGACTTACATTGTGA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 77.10% | 20.70% | 2.18% | 0.00% | NA |
| All Indica | 2759 | 89.60% | 9.00% | 1.38% | 0.00% | NA |
| All Japonica | 1512 | 58.30% | 38.00% | 3.77% | 0.00% | NA |
| Aus | 269 | 62.80% | 36.40% | 0.74% | 0.00% | NA |
| Indica I | 595 | 98.50% | 0.00% | 1.51% | 0.00% | NA |
| Indica II | 465 | 94.40% | 5.20% | 0.43% | 0.00% | NA |
| Indica III | 913 | 86.20% | 13.40% | 0.44% | 0.00% | NA |
| Indica Intermediate | 786 | 84.10% | 13.00% | 2.93% | 0.00% | NA |
| Temperate Japonica | 767 | 88.50% | 7.00% | 4.43% | 0.00% | NA |
| Tropical Japonica | 504 | 21.20% | 76.80% | 1.98% | 0.00% | NA |
| Japonica Intermediate | 241 | 39.40% | 55.20% | 5.39% | 0.00% | NA |
| VI/Aromatic | 96 | 65.60% | 32.30% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 63.30% | 32.20% | 4.44% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0421279302 | G -> A | LOC_Os04g35020.1 | downstream_gene_variant ; 2410.0bp to feature; MODIFIER | silent_mutation | Average:44.626; most accessible tissue: Callus, score: 85.473 | N | N | N | N |
| vg0421279302 | G -> A | LOC_Os04g35010.1 | intron_variant ; MODIFIER | silent_mutation | Average:44.626; most accessible tissue: Callus, score: 85.473 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0421279302 | NA | 4.29E-06 | mr1124 | 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 |
| vg0421279302 | NA | 9.66E-06 | mr1177 | 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 |
| vg0421279302 | NA | 1.48E-06 | mr1180 | 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 |
| vg0421279302 | NA | 2.95E-07 | mr1229 | 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 |