Variant ID: vg0727091375 (JBrowse) | Variation Type: SNP |
Chromosome: chr07 | Position: 27091375 |
Reference Allele: C | Alternative Allele: G |
Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GCGACCTCTCACGGTGGCTCCCTCCTCGGAGGTTGAGCAACCGCGACGCCTTACGGTGGCTCCCTCCACGGAGGTTGAGCAACCGTACGTTCCCCTCTTC[C/G]
GCCGACGCTTGCCGAACGACACCGTCCCTGCGGCACGTGACGCCCGATCAGCTGGCACGCCCTTGGTCAGCGCCTCCTCGATCGGCGCTGCCCCGTCGGT
ACCGACGGGGCAGCGCCGATCGAGGAGGCGCTGACCAAGGGCGTGCCAGCTGATCGGGCGTCACGTGCCGCAGGGACGGTGTCGTTCGGCAAGCGTCGGC[G/C]
GAAGAGGGGAACGTACGGTTGCTCAACCTCCGTGGAGGGAGCCACCGTAAGGCGTCGCGGTTGCTCAACCTCCGAGGAGGGAGCCACCGTGAGAGGTCGC
Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 95.70% | 4.30% | 0.00% | 0.00% | NA |
All Indica | 2759 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 94.00% | 6.00% | 0.00% | 0.00% | NA |
Aus | 269 | 65.10% | 34.90% | 0.00% | 0.00% | NA |
Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica III | 913 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 98.20% | 1.80% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 86.70% | 13.30% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 90.90% | 9.10% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 98.90% | 1.10% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0727091375 | C -> G | LOC_Os07g45410.1 | missense_variant ; p.Arg1589Gly; MODERATE | nonsynonymous_codon ; R1589G | Average:58.614; most accessible tissue: Zhenshan97 panicle, score: 76.605 | unknown | unknown | TOLERATED | 0.32 |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0727091375 | 2.17E-07 | 2.17E-07 | mr1200 | 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 |
vg0727091375 | NA | 1.44E-06 | mr1665 | 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 |