| Variant ID: vg0401517512 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 1517512 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TCTCATATCTTCAATATGCATACACTAAGGGGGAGTTTCATTCACCTCTAACCATTCAAAACAAAATTCTTATCAATCATTTGTAAGCTTTAACCATGTT[G/T]
TCATCAATCACCAAAAAGGGGGAGATTGAAAGTGCATTAATCCCCCTAGTGGGTTTTGGTGATTAATGACAAATGTGGTTAAGGGACTAATGAGTTCATT
AATGAACTCATTAGTCCCTTAACCACATTTGTCATTAATCACCAAAACCCACTAGGGGGATTAATGCACTTTCAATCTCCCCCTTTTTGGTGATTGATGA[C/A]
AACATGGTTAAAGCTTACAAATGATTGATAAGAATTTTGTTTTGAATGGTTAGAGGTGAATGAAACTCCCCCTTAGTGTATGCATATTGAAGATATGAGA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 94.70% | 2.80% | 2.54% | 0.00% | NA |
| All Indica | 2759 | 96.70% | 2.30% | 1.05% | 0.00% | NA |
| All Japonica | 1512 | 92.60% | 2.80% | 4.63% | 0.00% | NA |
| Aus | 269 | 88.50% | 7.10% | 4.46% | 0.00% | NA |
| Indica I | 595 | 96.80% | 2.40% | 0.84% | 0.00% | NA |
| Indica II | 465 | 96.60% | 2.20% | 1.29% | 0.00% | NA |
| Indica III | 913 | 96.60% | 2.30% | 1.10% | 0.00% | NA |
| Indica Intermediate | 786 | 96.70% | 2.30% | 1.02% | 0.00% | NA |
| Temperate Japonica | 767 | 99.10% | 0.40% | 0.52% | 0.00% | NA |
| Tropical Japonica | 504 | 83.10% | 6.20% | 10.71% | 0.00% | NA |
| Japonica Intermediate | 241 | 91.70% | 3.30% | 4.98% | 0.00% | NA |
| VI/Aromatic | 96 | 86.50% | 5.20% | 8.33% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 3.30% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0401517512 | G -> T | LOC_Os04g03490.1 | upstream_gene_variant ; 4997.0bp to feature; MODIFIER | silent_mutation | Average:12.81; most accessible tissue: Callus, score: 31.127 | N | N | N | N |
| vg0401517512 | G -> T | LOC_Os04g03490-LOC_Os04g03510 | intergenic_region ; MODIFIER | silent_mutation | Average:12.81; most accessible tissue: Callus, score: 31.127 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0401517512 | NA | 5.23E-06 | mr1534 | 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 |
| vg0401517512 | NA | 1.77E-06 | mr1064_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 |
| vg0401517512 | 1.80E-06 | NA | mr1871_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 |