Search for Variation information by Variation ID:
Detailed information for vg0617688888:
| Variant ID: vg0617688888 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 17688888 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TTCAGGTACTTACCACTGCAGGCCGATTCCAGCAGGATACTCCAAGGTCGAAGTTGAGTTGGTCGAAGGCGCGTACGAGGACCTCGAGCTAGATTACCCT[G/A]
GAGGAGACGGTGAGACGCATCTACGAGACACAAGCCATGCCATTATTCTATGGCACAGGCAGTACATCATCCTCCCTGGGCGACAAGCGGCGTCTCGTGC
Reverse complement sequence
GCACGAGACGCCGCTTGTCGCCCAGGGAGGATGATGTACTGCCTGTGCCATAGAATAATGGCATGGCTTGTGTCTCGTAGATGCGTCTCACCGTCTCCTC[C/T]
AGGGTAATCTAGCTCGAGGTCCTCGTACGCGCCTTCGACCAACTCAACTTCGACCTTGGAGTATCCTGCTGGAATCGGCCTGCAGTGGTAAGTACCTGAA
Allele Frequencies:
| 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 | 38.70% | 1.70% | 39.08% | 20.48% | NA |
| All Indica | 2759 | 10.00% | 2.80% | 55.56% | 31.64% | NA |
| All Japonica | 1512 | 94.20% | 0.10% | 4.43% | 1.32% | NA |
| Aus | 269 | 32.70% | 0.40% | 54.28% | 12.64% | NA |
| Indica I | 595 | 10.40% | 1.30% | 47.06% | 41.18% | NA |
| Indica II | 465 | 7.30% | 3.90% | 53.98% | 34.84% | NA |
| Indica III | 913 | 6.70% | 2.60% | 65.06% | 25.63% | NA |
| Indica Intermediate | 786 | 15.30% | 3.30% | 51.91% | 29.52% | NA |
| Temperate Japonica | 767 | 96.60% | 0.10% | 1.30% | 1.96% | NA |
| Tropical Japonica | 504 | 89.10% | 0.00% | 10.52% | 0.40% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.00% | 1.66% | 1.24% | NA |
| VI/Aromatic | 96 | 3.10% | 1.00% | 69.79% | 26.04% | NA |
| Intermediate | 90 | 41.10% | 3.30% | 37.78% | 17.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0617688888 | G -> A | LOC_Os06g30570.1 | missense_variant ; p.Gly536Arg; MODERATE | nonsynonymous_codon ; G536R | Average:7.673; most accessible tissue: Zhenshan97 root, score: 12.891 | benign  |
0.767 |
DELETERIOUS | 0.04 |
| vg0617688888 | G -> DEL | LOC_Os06g30570.1 | N | frameshift_variant | Average:7.673; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0617688888 | NA | 8.46E-06 | mr1291_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 |
| vg0617688888 | NA | 4.08E-06 | mr1543_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 |
| vg0617688888 | 3.25E-06 | 1.42E-07 | mr1931_2 | 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 |