Variant ID: vg0115227579 (JBrowse) | Variation Type: SNP |
Chromosome: chr01 | Position: 15227579 |
Reference Allele: C | Alternative Allele: A |
Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TTTCAATGGTCAAGTTGTGGATCAAACAGATCATGCTATTATCATGCAGTTTTCTGCCAGAGTTAGCCCTGATACCTTTAATCTGGTTAATGTTTATGGG[C/A]
CATCTTCTGGCCCCCAAAGAGATGATTTTGTTCACTGGATGAATGGGCTAGACATATATTTGAATGAAAACTGGATCTTTACGGGTGATTTCAATTTTTA
TAAAAATTGAAATCACCCGTAAAGATCCAGTTTTCATTCAAATATATGTCTAGCCCATTCATCCAGTGAACAAAATCATCTCTTTGGGGGCCAGAAGATG[G/T]
CCCATAAACATTAACCAGATTAAAGGTATCAGGGCTAACTCTGGCAGAAAACTGCATGATAATAGCATGATCTGTTTGATCCACAACTTGACCATTGAAA
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 | 34.90% | 7.00% | 10.77% | 47.33% | NA |
All Indica | 2759 | 3.80% | 11.40% | 17.00% | 67.81% | NA |
All Japonica | 1512 | 85.90% | 0.00% | 0.26% | 13.82% | NA |
Aus | 269 | 55.00% | 4.50% | 10.04% | 30.48% | NA |
Indica I | 595 | 3.00% | 18.30% | 20.17% | 58.49% | NA |
Indica II | 465 | 4.70% | 16.80% | 26.24% | 52.26% | NA |
Indica III | 913 | 2.00% | 3.80% | 10.08% | 84.12% | NA |
Indica Intermediate | 786 | 6.00% | 11.70% | 17.18% | 65.14% | NA |
Temperate Japonica | 767 | 95.00% | 0.00% | 0.26% | 4.69% | NA |
Tropical Japonica | 504 | 89.30% | 0.00% | 0.00% | 10.71% | NA |
Japonica Intermediate | 241 | 49.80% | 0.00% | 0.83% | 49.38% | NA |
VI/Aromatic | 96 | 47.90% | 0.00% | 2.08% | 50.00% | NA |
Intermediate | 90 | 55.60% | 6.70% | 7.78% | 30.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0115227579 | C -> A | LOC_Os01g27280.1 | missense_variant ; p.Pro570Thr; MODERATE | nonsynonymous_codon ; P570T | Average:11.145; most accessible tissue: Zhenshan97 young leaf, score: 30.745 | unknown | unknown | TOLERATED | 0.33 |
vg0115227579 | C -> DEL | LOC_Os01g27280.1 | N | frameshift_variant | Average:11.145; most accessible tissue: Zhenshan97 young leaf, score: 30.745 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0115227579 | NA | 1.11E-09 | mr1091 | 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 |
vg0115227579 | NA | 1.62E-10 | mr1065_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 |
vg0115227579 | NA | 6.38E-10 | mr1087_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 |
vg0115227579 | NA | 2.63E-11 | mr1091_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 |
vg0115227579 | NA | 3.38E-10 | mr1108_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 |
vg0115227579 | NA | 7.79E-27 | mr1877_2 | 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 |
vg0115227579 | NA | 1.42E-08 | mr1877_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 |