| Variant ID: vg0811678191 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11678191 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TCACATAGGAGTGGGATCTTGGTGAAGTTGTAGCCAAAGTCTTTTAGAGTTTGTTTCATCCAAAGGAGTTGGGCACAACAAGAACCGGCGGCGACATATT[C/T]
GGCTTCAGCGGTGGATAATGCAATGGAATTTTGCTTCTTGGAGGACCAAGAAACAAGGGACCGCCCAAGAAATTGGCAAGTCCCGGTTGTGCTTTTTCTA
TAGAAAAAGCACAACCGGGACTTGCCAATTTCTTGGGCGGTCCCTTGTTTCTTGGTCCTCCAAGAAGCAAAATTCCATTGCATTATCCACCGCTGAAGCC[G/A]
AATATGTCGCCGCCGGTTCTTGTTGTGCCCAACTCCTTTGGATGAAACAAACTCTAAAAGACTTTGGCTACAACTTCACCAAGATCCCACTCCTATGTGA
| 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 | 93.80% | 3.60% | 2.12% | 0.49% | NA |
| All Indica | 2759 | 96.50% | 0.30% | 2.90% | 0.29% | NA |
| All Japonica | 1512 | 87.80% | 9.90% | 1.32% | 0.99% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.70% | 0.00% | 1.18% | 0.17% | NA |
| Indica II | 465 | 97.40% | 0.00% | 2.15% | 0.43% | NA |
| Indica III | 913 | 95.20% | 0.40% | 4.38% | 0.00% | NA |
| Indica Intermediate | 786 | 95.90% | 0.50% | 2.93% | 0.64% | NA |
| Temperate Japonica | 767 | 95.60% | 0.30% | 2.22% | 1.96% | NA |
| Tropical Japonica | 504 | 73.60% | 26.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 92.50% | 6.20% | 1.24% | 0.00% | NA |
| VI/Aromatic | 96 | 92.70% | 7.30% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 5.60% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0811678191 | C -> T | LOC_Os08g19530.1 | missense_variant ; p.Glu121Lys; MODERATE | nonsynonymous_codon ; E121K | Average:36.453; most accessible tissue: Zhenshan97 flag leaf, score: 51.466 | unknown | unknown | TOLERATED | 0.08 |
| vg0811678191 | C -> DEL | LOC_Os08g19530.1 | N | frameshift_variant | Average:36.453; most accessible tissue: Zhenshan97 flag leaf, score: 51.466 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0811678191 | NA | 1.63E-07 | mr1134 | 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 |
| vg0811678191 | NA | 1.07E-06 | mr1135 | 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 |
| vg0811678191 | 5.91E-06 | 3.74E-08 | mr1504 | 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 |
| vg0811678191 | 1.10E-07 | 5.22E-09 | mr1134_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 |