| Variant ID: vg1125103445 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 25103445 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TTAGCACCGGAGTTACTACTGCCACCTCCATTAATCATTTCCGGGACTCTGTTTTTTGCATTAGTAGCACTAGCATTGCTCCTTGTAGAGATGTTCCTGC[A/C]
TTGTTGCTGTCTTGCAAGCCGCTTCCGATCAATGCCGTTCATTTCTTGCAATGTTATATCCATTTATTAGTTTTAGAAGAGCACCATCGGTCCATAAAAA
TTTTTATGGACCGATGGTGCTCTTCTAAAACTAATAAATGGATATAACATTGCAAGAAATGAACGGCATTGATCGGAAGCGGCTTGCAAGACAGCAACAA[T/G]
GCAGGAACATCTCTACAAGGAGCAATGCTAGTGCTACTAATGCAAAAAACAGAGTCCCGGAAATGATTAATGGAGGTGGCAGTAGTAACTCCGGTGCTAA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 66.20% | 4.50% | 23.44% | 5.90% | NA |
| All Indica | 2759 | 71.00% | 0.50% | 20.37% | 8.19% | NA |
| All Japonica | 1512 | 59.10% | 12.70% | 25.86% | 2.38% | NA |
| Aus | 269 | 53.50% | 0.00% | 41.64% | 4.83% | NA |
| Indica I | 595 | 64.40% | 0.20% | 16.81% | 18.66% | NA |
| Indica II | 465 | 64.90% | 1.30% | 24.30% | 9.46% | NA |
| Indica III | 913 | 75.70% | 0.10% | 21.25% | 2.96% | NA |
| Indica Intermediate | 786 | 74.00% | 0.60% | 19.72% | 5.60% | NA |
| Temperate Japonica | 767 | 52.30% | 22.30% | 23.73% | 1.69% | NA |
| Tropical Japonica | 504 | 69.20% | 1.00% | 25.60% | 4.17% | NA |
| Japonica Intermediate | 241 | 59.30% | 6.60% | 33.20% | 0.83% | NA |
| VI/Aromatic | 96 | 76.00% | 0.00% | 23.96% | 0.00% | NA |
| Intermediate | 90 | 65.60% | 7.80% | 22.22% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1125103445 | A -> DEL | LOC_Os11g41770.1 | N | frameshift_variant | Average:14.412; most accessible tissue: Callus, score: 27.826 | N | N | N | N |
| vg1125103445 | A -> C | LOC_Os11g41770.1 | missense_variant ; p.Cys15Gly; MODERATE | nonsynonymous_codon ; C15G | Average:14.412; most accessible tissue: Callus, score: 27.826 | unknown | unknown | TOLERATED | 0.66 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1125103445 | 6.51E-06 | NA | mr1926 | 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 |
| vg1125103445 | 1.81E-08 | NA | mr1310_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 |
| vg1125103445 | NA | 5.80E-06 | mr1768_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 |
| vg1125103445 | 4.30E-09 | 1.46E-06 | mr1959_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 |