Search for Variation information by Variation ID:
Detailed information for vg0322728335:
| Variant ID: vg0322728335 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 22728335 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GAAAGTCCAGCGACCGATCTACTTCGTTAGTGAAGTTTTGGCTGACTCCAAGACAAGATATCCTCAAGTTCAGAAGCTGTTGTACGGTGTCTTGATCACC[G/A]
TCAGGAAATTATCCCACTACTTCCAAGGTCACTCGGTCACGGTGGTTACATCGTTTCCACTCGGGGATATACTTCATAACCGCGAGGCAAATGGACGAAT
Reverse complement sequence
ATTCGTCCATTTGCCTCGCGGTTATGAAGTATATCCCCGAGTGGAAACGATGTAACCACCGTGACCGAGTGACCTTGGAAGTAGTGGGATAATTTCCTGA[C/T]
GGTGATCAAGACACCGTACAACAGCTTCTGAACTTGAGGATATCTTGTCTTGGAGTCAGCCAAAACTTCACTAACGAAGTAGATCGGTCGCTGGACTTTC
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 | 53.70% | 2.60% | 1.82% | 41.85% | NA |
| All Indica | 2759 | 28.30% | 0.10% | 2.50% | 69.08% | NA |
| All Japonica | 1512 | 91.00% | 7.40% | 1.06% | 0.53% | NA |
| Aus | 269 | 88.10% | 0.70% | 0.00% | 11.15% | NA |
| Indica I | 595 | 33.10% | 0.20% | 4.87% | 61.85% | NA |
| Indica II | 465 | 23.40% | 0.00% | 1.94% | 74.62% | NA |
| Indica III | 913 | 22.70% | 0.10% | 1.64% | 75.58% | NA |
| Indica Intermediate | 786 | 34.10% | 0.10% | 2.04% | 63.74% | NA |
| Temperate Japonica | 767 | 98.30% | 0.70% | 0.91% | 0.13% | NA |
| Tropical Japonica | 504 | 78.80% | 19.20% | 0.79% | 1.19% | NA |
| Japonica Intermediate | 241 | 93.40% | 4.10% | 2.07% | 0.41% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 57.80% | 5.60% | 1.11% | 35.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0322728335 | G -> A | LOC_Os03g40870.1 | missense_variant ; p.Val1073Ile; MODERATE | nonsynonymous_codon ; V1073I | Average:5.166; most accessible tissue: Callus, score: 8.201 | benign  |
0.378 |
TOLERATED | 0.14 |
| vg0322728335 | G -> DEL | LOC_Os03g40870.1 | N | frameshift_variant | Average:5.166; most accessible tissue: Callus, score: 8.201 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0322728335 | 2.51E-06 | 2.51E-06 | mr1448_2 | 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 |