Variant ID: vg0904668868 (JBrowse) | Variation Type: SNP |
Chromosome: chr09 | Position: 4668868 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGAGATGCTGTGGACCACAATGCTCGAGACGTTCACGCAACCCGTGGGTACGGAGAACATAGTGAAACAGTGGACTCTGAAGAAAATGGCAGAACAGTTC[C/T]
AGAGCTTGAAGGGAGATCTCTACAAGAAATACATCCTGAAGGGACTAACACCGAACTTCGACGTATTCCCAAAGGTAAGGGATCATTGGGATGAGTTCGT
ACGAACTCATCCCAATGATCCCTTACCTTTGGGAATACGTCGAAGTTCGGTGTTAGTCCCTTCAGGATGTATTTCTTGTAGAGATCTCCCTTCAAGCTCT[G/A]
GAACTGTTCTGCCATTTTCTTCAGAGTCCACTGTTTCACTATGTTCTCCGTACCCACGGGTTGCGTGAACGTCTCGAGCATTGTGGTCCACAGCATCTCT
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 | 74.70% | 8.80% | 12.19% | 4.27% | NA |
All Indica | 2759 | 76.50% | 4.40% | 13.81% | 5.33% | NA |
All Japonica | 1512 | 69.40% | 16.60% | 10.91% | 3.11% | NA |
Aus | 269 | 91.80% | 6.30% | 1.12% | 0.74% | NA |
Indica I | 595 | 74.80% | 3.00% | 15.29% | 6.89% | NA |
Indica II | 465 | 80.00% | 4.50% | 12.04% | 3.44% | NA |
Indica III | 913 | 75.70% | 5.80% | 12.60% | 5.91% | NA |
Indica Intermediate | 786 | 76.60% | 3.70% | 15.14% | 4.58% | NA |
Temperate Japonica | 767 | 92.60% | 0.70% | 1.96% | 4.82% | NA |
Tropical Japonica | 504 | 40.10% | 37.30% | 21.83% | 0.79% | NA |
Japonica Intermediate | 241 | 56.80% | 24.10% | 16.60% | 2.49% | NA |
VI/Aromatic | 96 | 63.50% | 19.80% | 14.58% | 2.08% | NA |
Intermediate | 90 | 71.10% | 10.00% | 14.44% | 4.44% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0904668868 | C -> T | LOC_Os09g08850.1 | N | stop_gained | Average:27.025; most accessible tissue: Zhenshan97 flag leaf, score: 78.259 | N | N | N | N |
vg0904668868 | C -> DEL | LOC_Os09g08850.1 | N | frameshift_variant | Average:27.025; most accessible tissue: Zhenshan97 flag leaf, score: 78.259 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0904668868 | 3.13E-07 | 4.12E-10 | mr1422 | 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 |
vg0904668868 | NA | 4.77E-09 | mr1449_2 | 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 |
vg0904668868 | 6.89E-07 | NA | mr1850_2 | 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 |