| Variant ID: vg0813611459 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 13611459 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GTTCAAAACGGGAAGCAGCTCCTTCAGATGTGTTCGTCGAACATCTTTACGAACCGACCGTGCCCAAAAAAGAGACAGTCGAAGCCATGGATACTCAAGG[C/T]
GTAAGCATGATCGAAGCTGACTGGAGAGAACTGTTTATAAAATTTTTGAGCAAACAAGAACTCCCTCAAGACAAAAATGAAGCTGAGCGGATTTCCAGGC
GCCTGGAAATCCGCTCAGCTTCATTTTTGTCTTGAGGGAGTTCTTGTTTGCTCAAAAATTTTATAAACAGTTCTCTCCAGTCAGCTTCGATCATGCTTAC[G/A]
CCTTGAGTATCCATGGCTTCGACTGTCTCTTTTTTGGGCACGGTCGGTTCGTAAAGATGTTCGACGAACACATCTGAAGGAGCTGCTTCCCGTTTTGAAC
| 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 | 94.50% | 4.00% | 1.14% | 0.34% | NA |
| All Indica | 2759 | 95.90% | 4.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 91.60% | 4.70% | 3.44% | 0.26% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 96.10% | 3.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 95.30% | 4.70% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 93.60% | 6.40% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 90.60% | 3.00% | 6.39% | 0.00% | NA |
| Tropical Japonica | 504 | 95.00% | 5.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 87.60% | 9.50% | 1.24% | 1.66% | NA |
| VI/Aromatic | 96 | 86.50% | 0.00% | 1.04% | 12.50% | NA |
| Intermediate | 90 | 91.10% | 7.80% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0813611459 | C -> T | LOC_Os08g22620.1 | synonymous_variant ; p.Gly893Gly; LOW | synonymous_codon | Average:40.124; most accessible tissue: Zhenshan97 flag leaf, score: 64.225 | N | N | N | N |
| vg0813611459 | C -> DEL | LOC_Os08g22620.1 | N | frameshift_variant | Average:40.124; most accessible tissue: Zhenshan97 flag leaf, score: 64.225 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0813611459 | NA | 6.65E-06 | mr1122 | Ind_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 |
| vg0813611459 | 1.94E-06 | 1.82E-09 | mr1134 | Ind_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 |
| vg0813611459 | 8.95E-08 | 2.21E-09 | mr1135 | Ind_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 |
| vg0813611459 | NA | 6.28E-08 | mr1504 | Ind_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 |
| vg0813611459 | 1.62E-06 | 4.78E-08 | mr1672 | Ind_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 |
| vg0813611459 | NA | 5.23E-08 | mr1134_2 | Ind_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 |
| vg0813611459 | 1.24E-06 | 1.24E-06 | mr1670_2 | Ind_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 |