Search for Variation information by Variation ID:
Detailed information for vg0907680153:
| Variant ID: vg0907680153 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 7680153 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GACGTTTTCAACTCCTACAATTCGGCGCTTTCCATCCCTCACGATGTGCATCTTCTTGTTTGAAGGGTCTTTTATGTAGAATATCTGCTCGACCTGTTTC[A/G]
CAAGTACAAATAGTTCATCGGCGTATCCCACCTTAGATAGATCAACTAAAGTGAAACCTTCCTTGTCGGCTTTGACACCAGTGCATATATTCACCCAATG
Reverse complement sequence
CATTGGGTGAATATATGCACTGGTGTCAAAGCCGACAAGGAAGGTTTCACTTTAGTTGATCTATCTAAGGTGGGATACGCCGATGAACTATTTGTACTTG[T/C]
GAAACAGGTCGAGCAGATATTCTACATAAAAGACCCTTCAAACAAGAAGATGCACATCGTGAGGGATGGAAAGCGCCGAATTGTAGGAGTTGAAAACGTC
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 40.10% | 3.60% | 1.04% | 55.27% | NA |
| All Indica | 2759 | 13.40% | 5.70% | 0.80% | 80.07% | NA |
| All Japonica | 1512 | 87.60% | 0.10% | 0.26% | 11.97% | NA |
| Aus | 269 | 17.80% | 2.60% | 7.81% | 71.75% | NA |
| Indica I | 595 | 17.80% | 0.50% | 0.84% | 80.84% | NA |
| Indica II | 465 | 9.20% | 1.50% | 0.43% | 88.82% | NA |
| Indica III | 913 | 9.70% | 13.00% | 0.66% | 76.56% | NA |
| Indica Intermediate | 786 | 16.80% | 3.70% | 1.15% | 78.37% | NA |
| Temperate Japonica | 767 | 78.40% | 0.00% | 0.39% | 21.25% | NA |
| Tropical Japonica | 504 | 98.60% | 0.00% | 0.00% | 1.39% | NA |
| Japonica Intermediate | 241 | 94.20% | 0.80% | 0.41% | 4.56% | NA |
| VI/Aromatic | 96 | 94.80% | 1.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 68.90% | 1.10% | 2.22% | 27.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0907680153 | A -> G | LOC_Os09g13320.1 | missense_variant ; p.Val426Ala; MODERATE | nonsynonymous_codon ; V426A | Average:6.627; most accessible tissue: Callus, score: 19.795 | benign  |
-0.404 |
TOLERATED | 1.00 |
| vg0907680153 | A -> DEL | LOC_Os09g13320.1 | N | frameshift_variant | Average:6.627; most accessible tissue: Callus, score: 19.795 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0907680153 | NA | 2.04E-06 | mr1358_2 | 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 |
| vg0907680153 | NA | 1.93E-06 | mr1754_2 | 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 |
| vg0907680153 | 1.57E-06 | 1.05E-07 | mr1882_2 | 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 |
| vg0907680153 | 9.50E-06 | 6.28E-06 | mr1882_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 |