Search for Variation information by Variation ID:
Detailed information for vg0614490153:
| Variant ID: vg0614490153 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 14490153 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ATCAGTCCAAACGTCATCTTAACGTAGCAGAATACACCGAACGGCGTGATGAATGCTGTCTTCTCCTCGTCCTCTTTCGCCATGCTGATTTGGTGGTAGC[T/C]
GGAGTAAGCGTCAAGAAAACTTAACAACTCACAACCAGCTGTTGAGTCCACCAGTTGGTCTATTCGAGGACGAGGGAAATGATACTTGGGACACGCCTTG
Reverse complement sequence
CAAGGCGTGTCCCAAGTATCATTTCCCTCGTCCTCGAATAGACCAACTGGTGGACTCAACAGCTGGTTGTGAGTTGTTAAGTTTTCTTGACGCTTACTCC[A/G]
GCTACCACCAAATCAGCATGGCGAAAGAGGACGAGGAGAAGACAGCATTCATCACGCCGTTCGGTGTATTCTGCTACGTTAAGATGACGTTTGGACTGAT
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 | 67.50% | 31.50% | 0.17% | 0.89% | NA |
| All Indica | 2759 | 96.40% | 2.90% | 0.14% | 0.58% | NA |
| All Japonica | 1512 | 7.20% | 90.80% | 0.26% | 1.72% | NA |
| Aus | 269 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 96.30% | 3.70% | 0.00% | 0.00% | NA |
| Indica II | 465 | 96.10% | 3.20% | 0.43% | 0.22% | NA |
| Indica III | 913 | 98.40% | 0.50% | 0.11% | 0.99% | NA |
| Indica Intermediate | 786 | 94.30% | 4.80% | 0.13% | 0.76% | NA |
| Temperate Japonica | 767 | 3.70% | 96.20% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 12.30% | 82.10% | 0.40% | 5.16% | NA |
| Japonica Intermediate | 241 | 7.90% | 91.70% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 66.70% | 33.30% | 0.00% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0614490153 | T -> C | LOC_Os06g24670.1 | missense_variant ; p.Ser53Gly; MODERATE | nonsynonymous_codon ; S53D | Average:45.666; most accessible tissue: Zhenshan97 flag leaf, score: 66.824 | benign  |
0.227 |
DELETERIOUS | 0.00 |
| vg0614490153 | T -> C | LOC_Os06g24670.1 | missense_variant ; p.Ser53Gly; MODERATE | nonsynonymous_codon ; S53G | Average:45.666; most accessible tissue: Zhenshan97 flag leaf, score: 66.824 | benign |
-0.69 |
TOLERATED | 1.00 |
| vg0614490153 | T -> DEL | LOC_Os06g24670.1 | N | frameshift_variant | Average:45.666; most accessible tissue: Zhenshan97 flag leaf, score: 66.824 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0614490153 | NA | 1.80E-07 | mr1190 | 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 |
| vg0614490153 | NA | 2.59E-06 | mr1445 | 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 |
| vg0614490153 | NA | 9.42E-12 | mr1806 | 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 |
| vg0614490153 | NA | 1.16E-10 | mr1986_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 |