Search for Variation information by Variation ID:
Detailed information for vg0912054345:
| Variant ID: vg0912054345 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 12054345 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AAGATTCACGCATGTCCGAATGATTGTATCCTATATCGCAGTGAGGAGTATGAGAACCTAGAAGCATGCCCTGTTTGTAAAGCACTACGATACAATATTA[A/G]
ACGAGAGGATCCAGGTGAAGTTGACGGGCAGCCAACAAAGAAGAGAATTCCTGCTAAGGTGATGTGGTATTTCCCCATAATACCACGGCTAAGGCGTTTG
Reverse complement sequence
CAAACGCCTTAGCCGTGGTATTATGGGGAAATACCACATCACCTTAGCAGGAATTCTCTTCTTTGTTGGCTGCCCGTCAACTTCACCTGGATCCTCTCGT[T/C]
TAATATTGTATCGTAGTGCTTTACAAACAGGGCATGCTTCTAGGTTCTCATACTCCTCACTGCGATATAGGATACAATCATTCGGACATGCGTGAATCTT
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 | 39.10% | 24.40% | 27.06% | 9.42% | NA |
| All Indica | 2759 | 44.40% | 3.10% | 40.92% | 11.60% | NA |
| All Japonica | 1512 | 33.10% | 65.90% | 0.40% | 0.53% | NA |
| Aus | 269 | 3.00% | 10.40% | 46.47% | 40.15% | NA |
| Indica I | 595 | 58.70% | 6.20% | 28.91% | 6.22% | NA |
| Indica II | 465 | 74.20% | 1.90% | 21.08% | 2.80% | NA |
| Indica III | 913 | 24.50% | 0.40% | 56.19% | 18.84% | NA |
| Indica Intermediate | 786 | 39.10% | 4.50% | 44.02% | 12.47% | NA |
| Temperate Japonica | 767 | 23.60% | 75.70% | 0.39% | 0.26% | NA |
| Tropical Japonica | 504 | 38.30% | 61.10% | 0.20% | 0.40% | NA |
| Japonica Intermediate | 241 | 52.70% | 44.80% | 0.83% | 1.66% | NA |
| VI/Aromatic | 96 | 74.00% | 11.50% | 7.29% | 7.29% | NA |
| Intermediate | 90 | 46.70% | 37.80% | 13.33% | 2.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0912054345 | A -> G | LOC_Os09g20120.1 | missense_variant ; p.Lys138Arg; MODERATE | nonsynonymous_codon ; K138R | Average:41.19; most accessible tissue: Zhenshan97 root, score: 60.612 | benign  |
-0.882 |
TOLERATED | 1.00 |
| vg0912054345 | A -> DEL | LOC_Os09g20120.1 | N | frameshift_variant | Average:41.19; most accessible tissue: Zhenshan97 root, score: 60.612 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0912054345 | 1.40E-06 | 2.84E-06 | mr1446_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 |