Search for Variation information by Variation ID:
Detailed information for vg0324105693:
| Variant ID: vg0324105693 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 24105693 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTGTGTTTGCTACATCATCGCCTCAAGATCATTCTTCTGTTCAGGTGTCAATTTGTCTACAGTGATAGGCACGATGTTGCTCTCATGAACTTCAGACCCA[C/A]
CAAGCTTCGGGATCCTAGATTTGGGAGGACCCTCTTTGCCAGCTGAGGACGGCGATGCTGGTGGTTTCTCAGCCATGAGAGAATGCTGTTGCGATTCTGA
Reverse complement sequence
TCAGAATCGCAACAGCATTCTCTCATGGCTGAGAAACCACCAGCATCGCCGTCCTCAGCTGGCAAAGAGGGTCCTCCCAAATCTAGGATCCCGAAGCTTG[G/T]
TGGGTCTGAAGTTCATGAGAGCAACATCGTGCCTATCACTGTAGACAAATTGACACCTGAACAGAAGAATGATCTTGAGGCGATGATGTAGCAAACACAG
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 53.70% | 43.30% | 2.05% | 1.02% | NA |
| All Indica | 2759 | 89.30% | 7.60% | 1.88% | 1.23% | NA |
| All Japonica | 1512 | 0.30% | 99.30% | 0.40% | 0.00% | NA |
| Aus | 269 | 13.80% | 78.40% | 3.72% | 4.09% | NA |
| Indica I | 595 | 88.70% | 9.60% | 1.34% | 0.34% | NA |
| Indica II | 465 | 89.00% | 8.60% | 1.72% | 0.65% | NA |
| Indica III | 913 | 93.20% | 2.20% | 2.63% | 1.97% | NA |
| Indica Intermediate | 786 | 85.40% | 11.70% | 1.53% | 1.40% | NA |
| Temperate Japonica | 767 | 0.10% | 99.60% | 0.26% | 0.00% | NA |
| Tropical Japonica | 504 | 0.20% | 99.20% | 0.60% | 0.00% | NA |
| Japonica Intermediate | 241 | 1.20% | 98.30% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 2.10% | 79.20% | 18.75% | 0.00% | NA |
| Intermediate | 90 | 31.10% | 53.30% | 12.22% | 3.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0324105693 | C -> A | LOC_Os03g43220.1 | missense_variant ; p.Gly26Val; MODERATE | nonsynonymous_codon ; G26L | Average:15.137; most accessible tissue: Callus, score: 30.23 | possibly damaging  |
1.907 |
TOLERATED | 0.07 |
| vg0324105693 | C -> DEL | LOC_Os03g43220.1 | N | frameshift_variant | Average:15.137; most accessible tissue: Callus, score: 30.23 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0324105693 | NA | 7.20E-06 | mr1555 | 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 |
| vg0324105693 | 1.29E-06 | 1.29E-06 | mr1555 | 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 |
| vg0324105693 | NA | 2.17E-11 | mr1938 | 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 |