| Variant ID: vg0422558702 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 22558702 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 272. )
CAAAGAATCTCCAAAAGTAGCAATGTCGGCGAAAGACTACAGACGAACCTCCGAGAGGATGGACTCCAGAACCACGGAGACCGAGGAGAGTGACTGTCAC[G/A]
CCCTGAAGTTTCCCCCTTTTCCTTGCTTTAAAATTTTGTTAAATAAATCGTCTGGAGAAATTGTTCTAATTAAGCTAGAGCTAATTCCTTAATTAATAAA
TTTATTAATTAAGGAATTAGCTCTAGCTTAATTAGAACAATTTCTCCAGACGATTTATTTAACAAAATTTTAAAGCAAGGAAAAGGGGGAAACTTCAGGG[C/T]
GTGACAGTCACTCTCCTCGGTCTCCGTGGTTCTGGAGTCCATCCTCTCGGAGGTTCGTCTGTAGTCTTTCGCCGACATTGCTACTTTTGGAGATTCTTTG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 93.00% | 6.90% | 0.15% | 0.00% | NA |
| All Indica | 2759 | 95.30% | 4.70% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 99.80% | 0.10% | 0.13% | 0.00% | NA |
| Aus | 269 | 31.60% | 68.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| Indica III | 913 | 95.10% | 4.90% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 90.10% | 9.80% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.20% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 92.70% | 6.20% | 1.04% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0422558702 | G -> A | LOC_Os04g37920.1 | downstream_gene_variant ; 3623.0bp to feature; MODIFIER | silent_mutation | Average:54.039; most accessible tissue: Zhenshan97 flag leaf, score: 64.768 | N | N | N | N |
| vg0422558702 | G -> A | LOC_Os04g37940.1 | downstream_gene_variant ; 4206.0bp to feature; MODIFIER | silent_mutation | Average:54.039; most accessible tissue: Zhenshan97 flag leaf, score: 64.768 | N | N | N | N |
| vg0422558702 | G -> A | LOC_Os04g37920.3 | downstream_gene_variant ; 3664.0bp to feature; MODIFIER | silent_mutation | Average:54.039; most accessible tissue: Zhenshan97 flag leaf, score: 64.768 | N | N | N | N |
| vg0422558702 | G -> A | LOC_Os04g37920.4 | downstream_gene_variant ; 3623.0bp to feature; MODIFIER | silent_mutation | Average:54.039; most accessible tissue: Zhenshan97 flag leaf, score: 64.768 | N | N | N | N |
| vg0422558702 | G -> A | LOC_Os04g37920.6 | downstream_gene_variant ; 3620.0bp to feature; MODIFIER | silent_mutation | Average:54.039; most accessible tissue: Zhenshan97 flag leaf, score: 64.768 | N | N | N | N |
| vg0422558702 | G -> A | LOC_Os04g37930.1 | intron_variant ; MODIFIER | silent_mutation | Average:54.039; most accessible tissue: Zhenshan97 flag leaf, score: 64.768 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0422558702 | NA | 5.16E-08 | mr1053 | 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 |
| vg0422558702 | NA | 1.54E-06 | mr1054 | 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 |
| vg0422558702 | NA | 1.69E-07 | mr1058 | 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 |
| vg0422558702 | NA | 1.34E-06 | mr1073 | 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 |
| vg0422558702 | NA | 1.10E-13 | mr1166 | 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 |
| vg0422558702 | NA | 1.20E-06 | mr1206 | 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 |
| vg0422558702 | NA | 3.38E-08 | mr1207 | 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 |
| vg0422558702 | NA | 3.32E-06 | mr1230 | 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 |
| vg0422558702 | NA | 1.24E-13 | mr1231 | 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 |
| vg0422558702 | NA | 3.48E-12 | mr1232 | 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 |
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