| Variant ID: vg1125905500 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 25905500 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, T: 0.09, others allele: 0.00, population size: 232. )
ACGAAGACGGCCGACCTAGTGCCCCGGCAGAAGCAGCCAAGAATTTTGTACGCCATAGCGGTTGGGTTGTGAGGGATAACGTGCCTGTCAGCCAGGTGTA[C/T]
TGGCGCAGAACAAGGACACGCGGGGATGATGACAGCTTTGTCCCGGAATCAGAGAAAGAGATGCTGTGGACCACAATGCTCGAGACGTTCACGCTCCCTG
CAGGGAGCGTGAACGTCTCGAGCATTGTGGTCCACAGCATCTCTTTCTCTGATTCCGGGACAAAGCTGTCATCATCCCCGCGTGTCCTTGTTCTGCGCCA[G/A]
TACACCTGGCTGACAGGCACGTTATCCCTCACAACCCAACCGCTATGGCGTACAAAATTCTTGGCTGCTTCTGCCGGGGCACTAGGTCGGCCGTCTTCGT
| 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 | 80.20% | 18.10% | 1.69% | 0.02% | NA |
| All Indica | 2759 | 71.90% | 25.80% | 2.21% | 0.04% | NA |
| All Japonica | 1512 | 95.40% | 3.30% | 1.26% | 0.00% | NA |
| Aus | 269 | 69.10% | 30.90% | 0.00% | 0.00% | NA |
| Indica I | 595 | 85.70% | 7.20% | 6.89% | 0.17% | NA |
| Indica II | 465 | 59.40% | 37.60% | 3.01% | 0.00% | NA |
| Indica III | 913 | 65.10% | 34.90% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 77.00% | 22.30% | 0.76% | 0.00% | NA |
| Temperate Japonica | 767 | 95.80% | 1.80% | 2.35% | 0.00% | NA |
| Tropical Japonica | 504 | 97.40% | 2.40% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 90.00% | 10.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 87.80% | 12.20% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1125905500 | C -> T | LOC_Os11g42980.1 | synonymous_variant ; p.Tyr135Tyr; LOW | synonymous_codon | Average:60.84; most accessible tissue: Zhenshan97 root, score: 73.6 | N | N | N | N |
| vg1125905500 | C -> DEL | LOC_Os11g42980.1 | N | frameshift_variant | Average:60.84; most accessible tissue: Zhenshan97 root, score: 73.6 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1125905500 | 5.54E-08 | 5.54E-08 | mr1644 | 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 |
| vg1125905500 | 3.08E-11 | 3.08E-11 | mr1191_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 |
| vg1125905500 | 4.61E-06 | 4.60E-06 | mr1367_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 |