Search for Variation information by Variation ID:
Detailed information for vg0906127537:
| Variant ID: vg0906127537 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 6127537 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGAAATCAGTCGGATACAGGGCCAAGCCAAAAGATTCCCGAGGTTGAAGCTCAAACAAATAGTCCTCCCGGGAAGGATGCTGGCAATGATTCAGAAACCA[G/A]
ATCTCCTGCGAAGACACAAGAGTCCACTCGTCCTCGACCAGGAATCATCACAGGTAAACACGCTATCTGAAATCATTACGATCCAACATACTTTATTTGA
Reverse complement sequence
TCAAATAAAGTATGTTGGATCGTAATGATTTCAGATAGCGTGTTTACCTGTGATGATTCCTGGTCGAGGACGAGTGGACTCTTGTGTCTTCGCAGGAGAT[C/T]
TGGTTTCTGAATCATTGCCAGCATCCTTCCCGGGAGGACTATTTGTTTGAGCTTCAACCTCGGGAATCTTTTGGCTTGGCCCTGTATCCGACTGATTTCC
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 | 69.90% | 5.00% | 3.55% | 21.52% | NA |
| All Indica | 2759 | 67.80% | 4.90% | 2.36% | 25.01% | NA |
| All Japonica | 1512 | 81.00% | 0.10% | 3.57% | 15.34% | NA |
| Aus | 269 | 39.80% | 35.70% | 17.10% | 7.43% | NA |
| Indica I | 595 | 91.10% | 0.20% | 1.85% | 6.89% | NA |
| Indica II | 465 | 48.40% | 0.40% | 1.08% | 50.11% | NA |
| Indica III | 913 | 63.50% | 10.50% | 2.30% | 23.66% | NA |
| Indica Intermediate | 786 | 66.50% | 4.50% | 3.56% | 25.45% | NA |
| Temperate Japonica | 767 | 90.50% | 0.00% | 0.52% | 9.00% | NA |
| Tropical Japonica | 504 | 78.40% | 0.20% | 9.13% | 12.30% | NA |
| Japonica Intermediate | 241 | 56.00% | 0.40% | 1.66% | 41.91% | NA |
| VI/Aromatic | 96 | 34.40% | 4.20% | 1.04% | 60.42% | NA |
| Intermediate | 90 | 76.70% | 2.20% | 2.22% | 18.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0906127537 | G -> DEL | LOC_Os09g11030.1 | N | frameshift_variant | Average:23.46; most accessible tissue: Zhenshan97 flag leaf, score: 51.466 | N | N | N | N |
| vg0906127537 | G -> A | LOC_Os09g11030.1 | missense_variant ; p.Arg331Lys; MODERATE | nonsynonymous_codon ; R331K | Average:23.46; most accessible tissue: Zhenshan97 flag leaf, score: 51.466 | benign  |
1.119 |
TOLERATED | 0.20 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0906127537 | NA | 1.91E-06 | mr1735 | 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 |
| vg0906127537 | 3.25E-06 | NA | mr1864 | 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 |