Search for Variation information by Variation ID:
Detailed information for vg1017280876:
| Variant ID: vg1017280876 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 17280876 |
| 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: 363. )
Flanking Sequence (100 bp) in Reference Genome:
AGGGTGTGCCACGGAGGCATAACAAATTTTAATGCCGAAGTCTTCACAAAAATCTTTAAATGCTCCGCCAGTGAATTGAGTGCCATTATCAGTGATGATC[C/T]
GATTAGGTACCCCAAACCGATGCACAATGTTGATGAAAAAATCTCTAACTTTATCTGCTGTGATCGTGATGACCGGTTTAGCCTCAATCCACTTGGAGAA
Reverse complement sequence
TTCTCCAAGTGGATTGAGGCTAAACCGGTCATCACGATCACAGCAGATAAAGTTAGAGATTTTTTCATCAACATTGTGCATCGGTTTGGGGTACCTAATC[G/A]
GATCATCACTGATAATGGCACTCAATTCACTGGCGGAGCATTTAAAGATTTTTGTGAAGACTTCGGCATTAAAATTTGTTATGCCTCCGTGGCACACCCT
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 | 96.60% | 3.10% | 0.32% | 0.00% | NA |
| All Indica | 2759 | 94.40% | 5.10% | 0.51% | 0.00% | NA |
| All Japonica | 1512 | 99.70% | 0.30% | 0.07% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 85.40% | 13.10% | 1.51% | 0.00% | NA |
| Indica II | 465 | 94.40% | 4.90% | 0.65% | 0.00% | NA |
| Indica III | 913 | 99.70% | 0.20% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 95.20% | 4.70% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.40% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 3.30% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1017280876 | C -> T | LOC_Os10g33010.1 | missense_variant ; p.Arg1512Gln; MODERATE | nonsynonymous_codon ; R1512Q | Average:20.279; most accessible tissue: Zhenshan97 flag leaf, score: 35.167 | benign  |
0.411 |
DELETERIOUS | 0.03 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1017280876 | NA | 1.34E-07 | Awn_length | Ind_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg1017280876 | 1.32E-06 | 3.45E-07 | mr1344 | 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 |
| vg1017280876 | NA | 5.29E-06 | mr1588 | 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 |
| vg1017280876 | 8.09E-06 | 5.46E-07 | mr1679 | 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 |
| vg1017280876 | NA | 1.47E-06 | mr1745 | 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 |
| vg1017280876 | 6.43E-06 | 6.43E-06 | mr1783 | 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 |
| vg1017280876 | NA | 5.08E-07 | mr1974 | 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 |