Search for Variation information by Variation ID:
Detailed information for vg0619963144:
| Variant ID: vg0619963144 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 19963144 |
| 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: 381. )
Flanking Sequence (100 bp) in Reference Genome:
ATTAGTCCGAACGGCATCTTAACATAGTAGAATACCCCGAACGGCGTGATGAATGCTGTCTTTTCCTCGTCCTCTTTCGCCATGCTGATTTGGTGGTAGC[C/T]
GGAGTAAGCGTCGAGAAAGCTCAACAACTCACAACCGGCTGTTGAGTCCACCAGTTGGTCTATTCGAGGAAGAGGGAAGTGATCCTTGGGACACTCCTTG
Reverse complement sequence
CAAGGAGTGTCCCAAGGATCACTTCCCTCTTCCTCGAATAGACCAACTGGTGGACTCAACAGCCGGTTGTGAGTTGTTGAGCTTTCTCGACGCTTACTCC[G/A]
GCTACCACCAAATCAGCATGGCGAAAGAGGACGAGGAAAAGACAGCATTCATCACGCCGTTCGGGGTATTCTACTATGTTAAGATGCCGTTCGGACTAAT
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 | 92.80% | 7.20% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 88.70% | 11.30% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 92.80% | 7.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 80.70% | 19.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 88.40% | 11.60% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 87.50% | 12.50% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 4.40% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0619963144 | C -> T | LOC_Os06g34320.1 | missense_variant ; p.Gly906Ser; MODERATE | nonsynonymous_codon ; G906S | Average:52.239; most accessible tissue: Minghui63 panicle, score: 71.773 | benign  |
1.202 |
DELETERIOUS | 0.04 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0619963144 | 2.39E-08 | 1.46E-10 | Awn_length | Ind_All | YES | 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 |
| vg0619963144 | NA | 5.12E-07 | mr1458 | 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 |
| vg0619963144 | NA | 6.23E-07 | mr1798 | 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 |
| vg0619963144 | NA | 2.68E-08 | mr1458_2 | 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 |
| vg0619963144 | NA | 1.04E-08 | mr1798_2 | 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 |