Variant ID: vg0714200726 (JBrowse) | Variation Type: SNP |
Chromosome: chr07 | Position: 14200726 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGTAATGTATCTGTGTTTCAGAGGGCATGGCTAGCAAATCCTGAGGCTAGCCAATATTTAGCATTTTTTTTTTCTGGAATTAACTCATCAGTGACGGGTC[G/A]
GAACAAAAATCCGTCAAAAGTAACCTAACCTGTGACGGACTAGCAAATAAAGGCCCGTCAGAGGTGACCTACCTGTGACGGGCCTTTACTTTTGGGGCCG
CGGCCCCAAAAGTAAAGGCCCGTCACAGGTAGGTCACCTCTGACGGGCCTTTATTTGCTAGTCCGTCACAGGTTAGGTTACTTTTGACGGATTTTTGTTC[C/T]
GACCCGTCACTGATGAGTTAATTCCAGAAAAAAAAAATGCTAAATATTGGCTAGCCTCAGGATTTGCTAGCCATGCCCTCTGAAACACAGATACATTACA
Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 96.50% | 0.80% | 1.18% | 1.50% | NA |
All Indica | 2759 | 97.20% | 1.40% | 1.41% | 0.00% | NA |
All Japonica | 1512 | 94.30% | 0.00% | 0.99% | 4.70% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 97.80% | 0.80% | 1.34% | 0.00% | NA |
Indica II | 465 | 95.30% | 2.40% | 2.37% | 0.00% | NA |
Indica III | 913 | 98.70% | 0.30% | 0.99% | 0.00% | NA |
Indica Intermediate | 786 | 96.20% | 2.40% | 1.40% | 0.00% | NA |
Temperate Japonica | 767 | 92.20% | 0.00% | 0.78% | 7.04% | NA |
Tropical Japonica | 504 | 97.20% | 0.00% | 1.19% | 1.59% | NA |
Japonica Intermediate | 241 | 95.00% | 0.00% | 1.24% | 3.73% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 97.80% | 0.00% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0714200726 | G -> DEL | LOC_Os07g24960.1 | N | frameshift_variant | Average:25.379; most accessible tissue: Minghui63 flag leaf, score: 42.036 | N | N | N | N |
vg0714200726 | G -> A | LOC_Os07g24960.1 | missense_variant ; p.Arg903Gln; MODERATE | nonsynonymous_codon ; R903Q | Average:25.379; most accessible tissue: Minghui63 flag leaf, score: 42.036 | unknown | unknown | TOLERATED | 0.45 |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0714200726 | 7.72E-06 | NA | mr1123 | Ind_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 |