| Variant ID: vg1124716076 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 24716076 |
| Reference Allele: C | Alternative Allele: T,A |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.67, T: 0.32, others allele: 0.00, population size: 281. )
TAATAAGATGATGGAGATTTGTGGAATTGGGAAGCTACTTCAGTTGCGGTACTTACGGATTGATCTAGTTACACATCTTACTGAAGAAATAGGAGAACTG[C/T,A]
TGTTTTTGGAGATATTGGATCTACCTCGTGGTATTGGTACAGAGGAGCTGCCCAAAGGCATAGTTAAACTGCGGCGGTTGAAATTTTTACACGTTCATGA
TCATGAACGTGTAAAAATTTCAACCGCCGCAGTTTAACTATGCCTTTGGGCAGCTCCTCTGTACCAATACCACGAGGTAGATCCAATATCTCCAAAAACA[G/A,T]
CAGTTCTCCTATTTCTTCAGTAAGATGTGTAACTAGATCAATCCGTAAGTACCGCAACTGAAGTAGCTTCCCAATTCCACAAATCTCCATCATCTTATTA
| 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 | 81.80% | 17.70% | 0.25% | 0.25% | NA |
| All Indica | 2759 | 81.80% | 17.70% | 0.33% | 0.18% | NA |
| All Japonica | 1512 | 87.10% | 12.80% | 0.07% | 0.00% | NA |
| Aus | 269 | 45.40% | 52.00% | 0.37% | 2.23% | NA |
| Indica I | 595 | 70.80% | 28.60% | 0.50% | 0.17% | NA |
| Indica II | 465 | 94.00% | 5.80% | 0.22% | 0.00% | NA |
| Indica III | 913 | 82.80% | 16.30% | 0.55% | 0.33% | NA |
| Indica Intermediate | 786 | 81.80% | 18.10% | 0.00% | 0.13% | NA |
| Temperate Japonica | 767 | 92.40% | 7.60% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 89.10% | 10.90% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 66.00% | 33.60% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 93.80% | 5.20% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 87.80% | 11.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1124716076 | C -> T | LOC_Os11g41210.1 | synonymous_variant ; p.Leu152Leu; LOW | synonymous_codon | Average:52.177; most accessible tissue: Minghui63 flag leaf, score: 77.153 | N | N | N | N |
| vg1124716076 | C -> A | LOC_Os11g41210.1 | missense_variant ; p.Leu152Met; MODERATE | N | Average:52.177; most accessible tissue: Minghui63 flag leaf, score: 77.153 | N | N | N | N |
| vg1124716076 | C -> DEL | LOC_Os11g41210.1 | N | frameshift_variant | Average:52.177; most accessible tissue: Minghui63 flag leaf, score: 77.153 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1124716076 | NA | 7.97E-06 | mr1807 | 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 |
| vg1124716076 | NA | 1.28E-08 | mr1531_2 | 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 |
| vg1124716076 | NA | 2.26E-06 | mr1788_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 |
| vg1124716076 | NA | 2.91E-07 | mr1807_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 |