| Variant ID: vg0432879824 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 32879824 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 34. )
TCCGGTAGTACGAATCGCTACGCTTCGCTTCTTTTTCACCGTCGGTTGCTGCGCTCCCTGCGGGTAATAGCAAGAGAGTGAAGAACGAACGATCATCAGT[T/C]
AGCAGTGAATGAGTCCGACTTGAGTTCGTGAGTCAAAGGCGTGGCAAGAGAGCGAGTTCGACTCGCGAACGACCTGCAAGTGAAGGACCGATCCTTTAAC
GTTAAAGGATCGGTCCTTCACTTGCAGGTCGTTCGCGAGTCGAACTCGCTCTCTTGCCACGCCTTTGACTCACGAACTCAAGTCGGACTCATTCACTGCT[A/G]
ACTGATGATCGTTCGTTCTTCACTCTCTTGCTATTACCCGCAGGGAGCGCAGCAACCGACGGTGAAAAAGAAGCGAAGCGTAGCGATTCGTACTACCGGA
| 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 | 28.10% | 0.10% | 9.06% | 62.70% | NA |
| All Indica | 2759 | 3.20% | 0.20% | 3.41% | 93.26% | NA |
| All Japonica | 1512 | 70.50% | 0.00% | 19.97% | 9.52% | NA |
| Aus | 269 | 44.20% | 0.40% | 1.12% | 54.28% | NA |
| Indica I | 595 | 4.00% | 0.20% | 2.86% | 92.94% | NA |
| Indica II | 465 | 2.40% | 0.20% | 3.23% | 94.19% | NA |
| Indica III | 913 | 1.40% | 0.10% | 5.59% | 92.88% | NA |
| Indica Intermediate | 786 | 5.00% | 0.30% | 1.40% | 93.38% | NA |
| Temperate Japonica | 767 | 90.50% | 0.00% | 8.74% | 0.78% | NA |
| Tropical Japonica | 504 | 44.20% | 0.00% | 30.36% | 25.40% | NA |
| Japonica Intermediate | 241 | 61.80% | 0.00% | 34.02% | 4.15% | NA |
| VI/Aromatic | 96 | 24.00% | 0.00% | 20.83% | 55.21% | NA |
| Intermediate | 90 | 37.80% | 0.00% | 10.00% | 52.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0432879824 | T -> C | LOC_Os04g55300-LOC_Os04g55310 | intergenic_region ; MODIFIER | silent_mutation | Average:10.951; most accessible tissue: Callus, score: 35.095 | N | N | N | N |
| vg0432879824 | T -> DEL | N | N | silent_mutation | Average:10.951; most accessible tissue: Callus, score: 35.095 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0432879824 | NA | 5.14E-06 | mr1448 | 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 |
| vg0432879824 | 5.49E-06 | 8.89E-09 | mr1072_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 |
| vg0432879824 | NA | 3.68E-07 | mr1075_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 |
| vg0432879824 | NA | 2.90E-08 | mr1077_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 |
| vg0432879824 | NA | 9.24E-06 | mr1149_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 |
| vg0432879824 | NA | 1.91E-07 | mr1441_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 |
| vg0432879824 | NA | 6.56E-07 | mr1568_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 |