Search for Variation information by Variation ID:
Detailed information for vg0629027841:
| Variant ID: vg0629027841 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 29027841 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TAGCCGGTGAGCTGGTCGAGGTTGAAGTTGCCATGAGGCAGGTTGACGCTGTTCCTGGTCGACACCCTGCCGTCGAACCTGCCGAGCTCCACCGCGTAGT[C/T]
CGGTCCTCCACTCTGCATCATGCAGCCAACCCATCAATGGCCATTCGTGCGTGTTCGAATATAAACTAAATTGCCAGTTTTCTCTTATGAGCTAAAACAT
Reverse complement sequence
ATGTTTTAGCTCATAAGAGAAAACTGGCAATTTAGTTTATATTCGAACACGCACGAATGGCCATTGATGGGTTGGCTGCATGATGCAGAGTGGAGGACCG[G/A]
ACTACGCGGTGGAGCTCGGCAGGTTCGACGGCAGGGTGTCGACCAGGAACAGCGTCAACCTGCCTCATGGCAACTTCAACCTCGACCAGCTCACCGGCTA
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 63.30% | 36.70% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 96.20% | 3.80% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 4.40% | 95.60% | 0.00% | 0.00% | NA |
| Aus | 269 | 45.00% | 55.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 90.80% | 9.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 97.40% | 2.60% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 95.70% | 4.30% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 3.00% | 97.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 6.50% | 93.50% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 4.10% | 95.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 93.80% | 6.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 65.60% | 34.40% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0629027841 | C -> T | LOC_Os06g48010.1 | missense_variant ; p.Asp141Asn; MODERATE | nonsynonymous_codon ; D141N | Average:71.941; most accessible tissue: Zhenshan97 panicle, score: 82.888 | benign  |
0.078 |
TOLERATED | 0.38 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0629027841 | NA | 2.54E-25 | mr1251 | 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 |
| vg0629027841 | NA | 8.19E-18 | mr1253 | 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 |
| vg0629027841 | NA | 4.18E-16 | mr1968 | 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 |
| vg0629027841 | NA | 2.20E-22 | mr1253_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 |
| vg0629027841 | NA | 8.14E-10 | mr1349_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 |