| Variant ID: vg1222490179 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 22490179 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TGCTAACCAACTCCATATCAAAACATATTTTCTAATTAGCTCATCCTCAGTATATTTGCTTAGAGACAACAAGCAAGTCTTCAAATGAAAAGGTAGATCG[C/T]
TGTAACTGAGGCTTAATATCTTCCGCATGTTGTCCACATCAAGGTTGTTCTCAAGCCCCAAACTGATAGACTTATTGACCTTGTCCCATTCCTCTGAATT
AATTCAGAGGAATGGGACAAGGTCAATAAGTCTATCAGTTTGGGGCTTGAGAACAACCTTGATGTGGACAACATGCGGAAGATATTAAGCCTCAGTTACA[G/A]
CGATCTACCTTTTCATTTGAAGACTTGCTTGTTGTCTCTAAGCAAATATACTGAGGATGAGCTAATTAGAAAATATGTTTTGATATGGAGTTGGTTAGCA
| 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 | 61.20% | 0.10% | 7.13% | 31.63% | NA |
| All Indica | 2759 | 52.20% | 0.00% | 8.88% | 38.93% | NA |
| All Japonica | 1512 | 82.50% | 0.10% | 4.89% | 12.50% | NA |
| Aus | 269 | 16.70% | 0.70% | 6.32% | 76.21% | NA |
| Indica I | 595 | 73.60% | 0.00% | 1.85% | 24.54% | NA |
| Indica II | 465 | 56.60% | 0.20% | 13.12% | 30.11% | NA |
| Indica III | 913 | 35.20% | 0.00% | 12.49% | 52.35% | NA |
| Indica Intermediate | 786 | 53.10% | 0.00% | 7.51% | 39.44% | NA |
| Temperate Japonica | 767 | 88.80% | 0.10% | 7.04% | 4.04% | NA |
| Tropical Japonica | 504 | 76.40% | 0.00% | 1.79% | 21.83% | NA |
| Japonica Intermediate | 241 | 75.50% | 0.00% | 4.56% | 19.92% | NA |
| VI/Aromatic | 96 | 90.60% | 0.00% | 1.04% | 8.33% | NA |
| Intermediate | 90 | 78.90% | 0.00% | 0.00% | 21.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1222490179 | C -> DEL | LOC_Os12g36720.1 | N | frameshift_variant | Average:42.981; most accessible tissue: Zhenshan97 flower, score: 66.436 | N | N | N | N |
| vg1222490179 | C -> T | LOC_Os12g36720.1 | missense_variant ; p.Ser409Asn; MODERATE | nonsynonymous_codon ; S409N | Average:42.981; most accessible tissue: Zhenshan97 flower, score: 66.436 | unknown | unknown | TOLERATED | 0.51 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1222490179 | NA | 5.83E-06 | mr1691 | 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 |
| vg1222490179 | NA | 5.19E-07 | mr1693 | 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 |
| vg1222490179 | 7.66E-06 | 5.38E-10 | mr1679_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 |
| vg1222490179 | NA | 1.61E-07 | mr1691_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 |
| vg1222490179 | 4.76E-06 | 1.04E-09 | mr1720_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 |