Search for Variation information by Variation ID:
Detailed information for vg1009912343:
| Variant ID: vg1009912343 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 9912343 |
| Reference Allele: A | Alternative Allele: G,T |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.00, others allele: 0.00, population size: 263. )
Flanking Sequence (100 bp) in Reference Genome:
CACCTCATGGGACATGAACTTTAAAATGCAGGCTGCTGGTGAGGAAGCGAAGTCAGTAGAAATATTAAAGCGCGACAAACTGATAGAATCATTAAGTGCC[A/G,T]
AATGTGCTGCTGCCAAGTCGGCTGCTCAAAGCGAACACGACAAAAATCTGCTACTCCAGAGGCAGTTGGATGATTCATTGAGAGAGATAACTATGTTGCG
Reverse complement sequence
CGCAACATAGTTATCTCTCTCAATGAATCATCCAACTGCCTCTGGAGTAGCAGATTTTTGTCGTGTTCGCTTTGAGCAGCCGACTTGGCAGCAGCACATT[T/C,A]
GGCACTTAATGATTCTATCAGTTTGTCGCGCTTTAATATTTCTACTGACTTCGCTTCCTCACCAGCAGCCTGCATTTTAAAGTTCATGTCCCATGAGGTG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 76.50% | 16.90% | 2.79% | 3.77% | T: 0.04% |
| All Indica | 2759 | 98.70% | 1.20% | 0.04% | 0.11% | NA |
| All Japonica | 1512 | 30.80% | 49.30% | 8.40% | 11.38% | T: 0.13% |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.70% | 0.20% | 0.17% | 0.00% | NA |
| Indica II | 465 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica III | 913 | 97.80% | 2.10% | 0.00% | 0.11% | NA |
| Indica Intermediate | 786 | 98.70% | 1.00% | 0.00% | 0.25% | NA |
| Temperate Japonica | 767 | 13.70% | 60.20% | 10.69% | 15.38% | NA |
| Tropical Japonica | 504 | 54.60% | 35.10% | 4.96% | 4.96% | T: 0.40% |
| Japonica Intermediate | 241 | 35.30% | 44.40% | 8.30% | 12.03% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 72.20% | 20.00% | 4.44% | 3.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1009912343 | A -> G | LOC_Os10g19860.1 | N | nonsynonymous_codon ; K399E | Average:47.931; most accessible tissue: Zhenshan97 young leaf, score: 61.386 | benign  |
-0.917 |
TOLERATED | 0.85 |
| vg1009912343 | A -> T | LOC_Os10g19860.1 | stop_gained ; p.Lys399*; HIGH | stop_gained | Average:47.931; most accessible tissue: Zhenshan97 young leaf, score: 61.386 | N | N | N | N |
| vg1009912343 | A -> DEL | LOC_Os10g19860.1 | N | frameshift_variant | Average:47.931; most accessible tissue: Zhenshan97 young leaf, score: 61.386 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1009912343 | NA | 3.59E-07 | mr1495 | Jap_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 |
| vg1009912343 | NA | 4.63E-07 | mr1622 | 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 |
| vg1009912343 | NA | 6.51E-06 | mr1704 | 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 |
| vg1009912343 | 3.86E-06 | 6.32E-20 | mr1768 | 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 |
| vg1009912343 | 1.38E-06 | NA | mr1027_2 | 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 |
| vg1009912343 | NA | 2.10E-06 | mr1027_2 | Jap_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 |
| vg1009912343 | NA | 2.41E-08 | mr1495_2 | Jap_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 |
| vg1009912343 | NA | 9.29E-30 | mr1768_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 |