Search for Variation information by Variation ID:
Detailed information for vg1000798980:
| Variant ID: vg1000798980 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 798980 |
| Reference Allele: T | Alternative Allele: A,G |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 41. )
Flanking Sequence (100 bp) in Reference Genome:
GGTGACGCAGCCGGCGTAGTAGAGGCTTGTGTAGAGGCCTTTTCCCTCGCTGTCCCCGTGCTTGTTCCATGCCACGGTGTTGCATCCCAGGACGACGAAC[T/A,G]
TGTTGCGCTCGTCGGAGATGCGGTACACGCCGGTCTTGTTCAGCTCCACGTCGCCGTAGAACTGCTCGGTGACGTTGCCGCTGGAGTTGTAGCACCTGTA
Reverse complement sequence
TACAGGTGCTACAACTCCAGCGGCAACGTCACCGAGCAGTTCTACGGCGACGTGGAGCTGAACAAGACCGGCGTGTACCGCATCTCCGACGAGCGCAACA[A/T,C]
GTTCGTCGTCCTGGGATGCAACACCGTGGCATGGAACAAGCACGGGGACAGCGAGGGAAAAGGCCTCTACACAAGCCTCTACTACGCCGGCTGCGTCACC
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 51.00% | 48.70% | 0.21% | 0.00% | G: 0.11% |
| All Indica | 2759 | 51.10% | 48.50% | 0.22% | 0.00% | G: 0.14% |
| All Japonica | 1512 | 51.00% | 48.70% | 0.20% | 0.00% | G: 0.07% |
| Aus | 269 | 39.00% | 61.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 64.00% | 36.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 25.20% | 74.40% | 0.43% | 0.00% | NA |
| Indica III | 913 | 51.00% | 48.40% | 0.11% | 0.00% | G: 0.44% |
| Indica Intermediate | 786 | 56.90% | 42.70% | 0.38% | 0.00% | NA |
| Temperate Japonica | 767 | 78.00% | 21.80% | 0.26% | 0.00% | NA |
| Tropical Japonica | 504 | 8.30% | 91.30% | 0.20% | 0.00% | G: 0.20% |
| Japonica Intermediate | 241 | 54.40% | 45.60% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 90.60% | 9.40% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 40.00% | 58.90% | 1.11% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1000798980 | T -> G | LOC_Os10g02250.1 | missense_variant ; p.Lys130Thr; MODERATE | nonsynonymous_codon ; K130T | Average:73.291; most accessible tissue: Zhenshan97 panicle, score: 83.904 | benign  |
0.248 |
TOLERATED | 0.63 |
| vg1000798980 | T -> A | LOC_Os10g02250.1 | missense_variant ; p.Lys130Met; MODERATE | nonsynonymous_codon ; K130V | Average:73.291; most accessible tissue: Zhenshan97 panicle, score: 83.904 | benign |
0.2 |
TOLERATED | 0.46 |
| vg1000798980 | T -> A | LOC_Os10g02250.1 | missense_variant ; p.Lys130Met; MODERATE | nonsynonymous_codon ; K130M | Average:73.291; most accessible tissue: Zhenshan97 panicle, score: 83.904 | benign |
0.315 |
TOLERATED | 0.31 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1000798980 | NA | 6.02E-06 | mr1286 | 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 |
| vg1000798980 | NA | 2.81E-06 | mr1677 | 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 |
| vg1000798980 | 1.12E-06 | 1.12E-06 | mr1777 | 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 |