| Variant ID: vg0411852309 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 11852309 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 80. )
TGCGACCATACTAGGTTGTTTGCTTAAGCAACTTGAATCATAAAATCCATTCACAACAGATCAATAGGCAAGTGGTTTAGTACCTCCTCTCTAGTAACCC[C/G]
TCCTATTTCCCCATCTCTCTATTGCCTGCAGCAGATGGTCCGCATGAGGGACAATTTCATCGGATCAAGACCCCGTCAGTTTCATGGGGCAACTCAGTGC
GCACTGAGTTGCCCCATGAAACTGACGGGGTCTTGATCCGATGAAATTGTCCCTCATGCGGACCATCTGCTGCAGGCAATAGAGAGATGGGGAAATAGGA[G/C]
GGGTTACTAGAGAGGAGGTACTAAACCACTTGCCTATTGATCTGTTGTGAATGGATTTTATGATTCAAGTTGCTTAAGCAAACAACCTAGTATGGTCGCA
| 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 | 34.60% | 9.30% | 20.69% | 35.34% | NA |
| All Indica | 2759 | 26.80% | 15.70% | 24.90% | 32.58% | NA |
| All Japonica | 1512 | 51.40% | 0.20% | 2.25% | 46.16% | NA |
| Aus | 269 | 6.30% | 0.00% | 81.04% | 12.64% | NA |
| Indica I | 595 | 4.20% | 30.40% | 26.22% | 39.16% | NA |
| Indica II | 465 | 41.50% | 22.20% | 21.08% | 15.27% | NA |
| Indica III | 913 | 38.00% | 1.80% | 23.11% | 37.13% | NA |
| Indica Intermediate | 786 | 22.30% | 16.90% | 28.24% | 32.57% | NA |
| Temperate Japonica | 767 | 85.10% | 0.00% | 0.39% | 14.47% | NA |
| Tropical Japonica | 504 | 5.80% | 0.20% | 5.36% | 88.69% | NA |
| Japonica Intermediate | 241 | 39.40% | 0.80% | 1.66% | 58.09% | NA |
| VI/Aromatic | 96 | 69.80% | 0.00% | 18.75% | 11.46% | NA |
| Intermediate | 90 | 40.00% | 5.60% | 23.33% | 31.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0411852309 | C -> DEL | N | N | silent_mutation | Average:34.16; most accessible tissue: Minghui63 flag leaf, score: 64.284 | N | N | N | N |
| vg0411852309 | C -> G | LOC_Os04g21090.1 | upstream_gene_variant ; 244.0bp to feature; MODIFIER | silent_mutation | Average:34.16; most accessible tissue: Minghui63 flag leaf, score: 64.284 | N | N | N | N |
| vg0411852309 | C -> G | LOC_Os04g21080-LOC_Os04g21090 | intergenic_region ; MODIFIER | silent_mutation | Average:34.16; most accessible tissue: Minghui63 flag leaf, score: 64.284 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0411852309 | 1.43E-06 | NA | mr1549 | 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 |
| vg0411852309 | NA | 2.41E-06 | mr1549_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 |
| vg0411852309 | NA | 7.03E-07 | mr1654_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 |
| vg0411852309 | NA | 4.24E-06 | mr1654_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 |
| vg0411852309 | NA | 5.14E-06 | mr1757_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 |