| Variant ID: vg0508296043 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 8296043 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, A: 0.03, others allele: 0.00, population size: 105. )
TTATTCATATAAAAATCATAAAATATTACACCAAATAATTCTTATTTACTATTTCTAAAGTTTTAAACTAATTTTAATATGTTTTACTTCTTTTAATTTT[C/T]
ATTTTAGTTTGTTTTCTAGTATTCAAGATTAACTTTCACTATAGTTTTCCTTCTCAACTATTTTATAAAACCTTCTTTAGCAAATCAACTAAATTTCTAT
ATAGAAATTTAGTTGATTTGCTAAAGAAGGTTTTATAAAATAGTTGAGAAGGAAAACTATAGTGAAAGTTAATCTTGAATACTAGAAAACAAACTAAAAT[G/A]
AAAATTAAAAGAAGTAAAACATATTAAAATTAGTTTAAAACTTTAGAAATAGTAAATAAGAATTATTTGGTGTAATATTTTATGATTTTTATATGAATAA
| 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 | 69.80% | 29.90% | 0.30% | 0.00% | NA |
| All Indica | 2759 | 52.70% | 46.80% | 0.47% | 0.00% | NA |
| All Japonica | 1512 | 93.80% | 6.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 97.40% | 2.60% | 0.00% | 0.00% | NA |
| Indica I | 595 | 43.50% | 55.80% | 0.67% | 0.00% | NA |
| Indica II | 465 | 58.50% | 41.30% | 0.22% | 0.00% | NA |
| Indica III | 913 | 55.60% | 43.90% | 0.44% | 0.00% | NA |
| Indica Intermediate | 786 | 52.90% | 46.60% | 0.51% | 0.00% | NA |
| Temperate Japonica | 767 | 92.30% | 7.70% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 86.30% | 13.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 77.80% | 21.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0508296043 | C -> T | LOC_Os05g14570.1 | upstream_gene_variant ; 4979.0bp to feature; MODIFIER | silent_mutation | Average:12.674; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| vg0508296043 | C -> T | LOC_Os05g14560.1 | intron_variant ; MODIFIER | silent_mutation | Average:12.674; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0508296043 | NA | 3.23E-08 | mr1593 | Ind_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 |
| vg0508296043 | 4.99E-07 | NA | mr1593_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 |
| vg0508296043 | 2.57E-07 | 6.97E-11 | mr1593_2 | Ind_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 |