Variant ID: vg0818600407 (JBrowse) | Variation Type: SNP |
Chromosome: chr08 | Position: 18600407 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TAGGTTCTTTTAATGGATTGACGTCCTACCTTATCCTTTTACAGCTGCGTTTTAAGTTTGCTGATGGTAGAGAAGTGGATTGTGCTAGATTATTTTATCG[C/T]
AAAGCTGTTGAACGTTTTAGCCAAGCTTTGTCACATGAGAAATCTGAAGCAAAACGTTCTTTGGAAAAGCATATCGAAAATATGCGTGCGACTGAGTTAC
GTAACTCAGTCGCACGCATATTTTCGATATGCTTTTCCAAAGAACGTTTTGCTTCAGATTTCTCATGTGACAAAGCTTGGCTAAAACGTTCAACAGCTTT[G/A]
CGATAAAATAATCTAGCACAATCCACTTCTCTACCATCAGCAAACTTAAAACGCAGCTGTAAAAGGATAAGGTAGGACGTCAATCCATTAAAAGAACCTA
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 | 94.80% | 3.70% | 0.74% | 0.68% | NA |
All Indica | 2759 | 98.50% | 1.00% | 0.54% | 0.00% | NA |
All Japonica | 1512 | 87.00% | 9.70% | 1.19% | 2.12% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Indica II | 465 | 98.90% | 0.90% | 0.22% | 0.00% | NA |
Indica III | 913 | 97.80% | 1.30% | 0.88% | 0.00% | NA |
Indica Intermediate | 786 | 98.00% | 1.30% | 0.76% | 0.00% | NA |
Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 65.30% | 26.80% | 2.78% | 5.16% | NA |
Japonica Intermediate | 241 | 91.30% | 4.60% | 1.66% | 2.49% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 93.30% | 4.40% | 2.22% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0818600407 | C -> T | LOC_Os08g30260.1 | synonymous_variant ; p.Arg201Arg; LOW | synonymous_codon | Average:22.116; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |
vg0818600407 | C -> DEL | LOC_Os08g30260.1 | N | frameshift_variant | Average:22.116; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0818600407 | NA | 1.02E-06 | mr1073 | 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 |
vg0818600407 | 2.89E-08 | 2.89E-08 | mr1266 | 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 |
vg0818600407 | NA | 1.33E-06 | mr1345 | 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 |
vg0818600407 | NA | 2.47E-06 | mr1638 | 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 |
vg0818600407 | 1.02E-06 | 5.83E-10 | mr1830 | 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 |
vg0818600407 | NA | 7.43E-07 | mr1852 | 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 |
vg0818600407 | NA | 1.69E-06 | mr1866 | 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 |
vg0818600407 | NA | 2.50E-08 | mr1047_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 |