Search for Variation information by Variation ID:
Detailed information for vg1016945482:
| Variant ID: vg1016945482 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 16945482 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 336. )
Flanking Sequence (100 bp) in Reference Genome:
AAGATTAGCACGGATCAACAGTTCTTTCCTTACTTCCAAAATTGCTTGGGGGCTATCGACGGAACACATGTTCCTATCACCATTTCTCAAGACCTTCAGG[C/T]
CCCATATAGGAATAGAAAGGGTACCCTAAGTCAAAATGTGATGTTGGTTTGTGATTTTGATCTAAATTTTTCGTTTATATCATCTGGATGGGAGGGATCT
Reverse complement sequence
AGATCCCTCCCATCCAGATGATATAAACGAAAAATTTAGATCAAAATCACAAACCAACATCACATTTTGACTTAGGGTACCCTTTCTATTCCTATATGGG[G/A]
CCTGAAGGTCTTGAGAAATGGTGATAGGAACATGTGTTCCGTCGATAGCCCCCAAGCAATTTTGGAAGTAAGGAAAGAACTGTTGATCCGTGCTAATCTT
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 94.80% | 4.60% | 0.04% | 0.53% | NA |
| All Indica | 2759 | 92.30% | 7.60% | 0.07% | 0.04% | NA |
| All Japonica | 1512 | 99.50% | 0.30% | 0.00% | 0.13% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 79.00% | 20.80% | 0.17% | 0.00% | NA |
| Indica II | 465 | 92.70% | 7.10% | 0.22% | 0.00% | NA |
| Indica III | 913 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 93.50% | 6.40% | 0.00% | 0.13% | NA |
| Temperate Japonica | 767 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 79.20% | 0.00% | 0.00% | 20.83% | NA |
| Intermediate | 90 | 94.40% | 3.30% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1016945482 | C -> T | LOC_Os10g32290.1 | missense_variant ; p.Ala59Val; MODERATE | nonsynonymous_codon ; A59V | Average:25.702; most accessible tissue: Minghui63 panicle, score: 42.799 | benign  |
0.747 |
DELETERIOUS | 0.03 |
| vg1016945482 | C -> DEL | LOC_Os10g32290.1 | N | frameshift_variant | Average:25.702; most accessible tissue: Minghui63 panicle, score: 42.799 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1016945482 | 2.42E-06 | NA | mr1005 | 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 |
| vg1016945482 | 3.14E-06 | 1.04E-06 | mr1005 | Ind_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 |
| vg1016945482 | NA | 1.29E-06 | mr1389 | 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 |
| vg1016945482 | NA | 9.40E-07 | mr1693 | Ind_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 |