| Variant ID: vg0509682776 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 9682776 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TACAAAGAGATGTCGCACTCTCGCAGTGGCGGCGGACGGTTTACGGCGCAAACCGACAAAGATGGACAAACTAAGAGAAAACTAAAAGCAATATGAAAAA[C/T]
GATTCGATTGATTGATTGTAGATTAGTTTTTTACAATGAACATGCCATGTCCCTTATATAGGGGTTGGTCTTGCCCTCTATAGGCCCTCCTCCACGTCCA
TGGACGTGGAGGAGGGCCTATAGAGGGCAAGACCAACCCCTATATAAGGGACATGGCATGTTCATTGTAAAAAACTAATCTACAATCAATCAATCGAATC[G/A]
TTTTTCATATTGCTTTTAGTTTTCTCTTAGTTTGTCCATCTTTGTCGGTTTGCGCCGTAAACCGTCCGCCGCCACTGCGAGAGTGCGACATCTCTTTGTA
| 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 | 89.10% | 9.60% | 1.29% | 0.00% | NA |
| All Indica | 2759 | 88.90% | 10.70% | 0.43% | 0.00% | NA |
| All Japonica | 1512 | 99.70% | 0.30% | 0.07% | 0.00% | NA |
| Aus | 269 | 27.10% | 56.10% | 16.73% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Indica III | 913 | 76.20% | 23.30% | 0.44% | 0.00% | NA |
| Indica Intermediate | 786 | 89.60% | 9.40% | 1.02% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 5.60% | 3.33% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0509682776 | C -> T | LOC_Os05g16970.1 | upstream_gene_variant ; 87.0bp to feature; MODIFIER | silent_mutation | Average:42.885; most accessible tissue: Minghui63 flag leaf, score: 59.912 | N | N | N | N |
| vg0509682776 | C -> T | LOC_Os05g16970-LOC_Os05g16980 | intergenic_region ; MODIFIER | silent_mutation | Average:42.885; most accessible tissue: Minghui63 flag leaf, score: 59.912 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0509682776 | 4.23E-06 | NA | mr1304_2 | 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 |
| vg0509682776 | 5.90E-07 | NA | mr1386_2 | 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 |
| vg0509682776 | NA | 5.79E-06 | mr1743_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 |