| Variant ID: vg0319912427 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 19912427 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CCGGAAATTCACTAGTAATTTCCGAACTTATTTGTGCATAAAACCCTCGTCTAGGAATCAGCCGAGGTACACAAACTGACAATTCAATATACAAATCCAT[G/C]
ATAATAATAACGTTACATACTCACAAAAGAAAAGAAAACAGCAGCGGAATAACGGTCTAGCGATGGCTTCAGCTCCACTCTCACAGGCAGCTCAACTGGG
CCCAGTTGAGCTGCCTGTGAGAGTGGAGCTGAAGCCATCGCTAGACCGTTATTCCGCTGCTGTTTTCTTTTCTTTTGTGAGTATGTAACGTTATTATTAT[C/G]
ATGGATTTGTATATTGAATTGTCAGTTTGTGTACCTCGGCTGATTCCTAGACGAGGGTTTTATGCACAAATAAGTTCGGAAATTACTAGTGAATTTCCGG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 67.50% | 31.40% | 0.72% | 0.34% | NA |
| All Indica | 2759 | 97.20% | 2.50% | 0.33% | 0.00% | NA |
| All Japonica | 1512 | 13.00% | 84.70% | 1.26% | 1.06% | NA |
| Aus | 269 | 90.00% | 10.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.80% | 1.80% | 0.34% | 0.00% | NA |
| Indica II | 465 | 97.00% | 2.80% | 0.22% | 0.00% | NA |
| Indica III | 913 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 95.20% | 4.10% | 0.76% | 0.00% | NA |
| Temperate Japonica | 767 | 0.50% | 97.40% | 0.00% | 2.09% | NA |
| Tropical Japonica | 504 | 34.30% | 65.50% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 7.90% | 84.60% | 7.47% | 0.00% | NA |
| VI/Aromatic | 96 | 25.00% | 72.90% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 52.20% | 43.30% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0319912427 | G -> C | LOC_Os03g35886.1 | upstream_gene_variant ; 3870.0bp to feature; MODIFIER | silent_mutation | Average:62.434; most accessible tissue: Zhenshan97 flag leaf, score: 78.512 | N | N | N | N |
| vg0319912427 | G -> C | LOC_Os03g35894.1 | downstream_gene_variant ; 3698.0bp to feature; MODIFIER | silent_mutation | Average:62.434; most accessible tissue: Zhenshan97 flag leaf, score: 78.512 | N | N | N | N |
| vg0319912427 | G -> C | LOC_Os03g35886-LOC_Os03g35894 | intergenic_region ; MODIFIER | silent_mutation | Average:62.434; most accessible tissue: Zhenshan97 flag leaf, score: 78.512 | N | N | N | N |
| vg0319912427 | G -> DEL | N | N | silent_mutation | Average:62.434; most accessible tissue: Zhenshan97 flag leaf, score: 78.512 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0319912427 | NA | 2.64E-10 | mr1188 | 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 |
| vg0319912427 | NA | 3.57E-07 | mr1227 | 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 |
| vg0319912427 | 1.67E-06 | NA | mr1333 | 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 |
| vg0319912427 | NA | 1.42E-16 | mr1933 | 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 |