Search for Variation information by Variation ID:
Detailed information for vg1126916922:
| Variant ID: vg1126916922 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26916922 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.73, T: 0.27, others allele: 0.00, population size: 89. )
Flanking Sequence (100 bp) in Reference Genome:
TTCAGAGCAAGATCGACTCGTACCTCCTCGTCTTCCCCTTCATCAGCCACATCGACATCACCCGCCGCCTCGATCGAATCTACAGAGTTCTTCTTCCAAA[T/C]
GACACGACCCTGCCATCCGCATCTGCAGGAATCCCGAATCATGAGATGGTACTACAAATTTTAAGCAATTTTATAGTTCTTGAGGAGGTATAAATTTTAA
Reverse complement sequence
TTAAAATTTATACCTCCTCAAGAACTATAAAATTGCTTAAAATTTGTAGTACCATCTCATGATTCGGGATTCCTGCAGATGCGGATGGCAGGGTCGTGTC[A/G]
TTTGGAAGAAGAACTCTGTAGATTCGATCGAGGCGGCGGGTGATGTCGATGTGGCTGATGAAGGGGAAGACGAGGAGGTACGAGTCGATCTTGCTCTGAA
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 | 66.10% | 27.40% | 0.38% | 6.14% | NA |
| All Indica | 2759 | 65.90% | 23.50% | 0.51% | 10.15% | NA |
| All Japonica | 1512 | 60.80% | 38.80% | 0.20% | 0.20% | NA |
| Aus | 269 | 84.80% | 13.80% | 0.37% | 1.12% | NA |
| Indica I | 595 | 43.40% | 29.60% | 0.17% | 26.89% | NA |
| Indica II | 465 | 85.20% | 14.60% | 0.00% | 0.22% | NA |
| Indica III | 913 | 70.60% | 20.50% | 0.99% | 7.89% | NA |
| Indica Intermediate | 786 | 66.00% | 27.50% | 0.51% | 5.98% | NA |
| Temperate Japonica | 767 | 34.80% | 64.50% | 0.39% | 0.26% | NA |
| Tropical Japonica | 504 | 95.60% | 4.20% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 70.50% | 29.50% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 1.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 73.30% | 23.30% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1126916922 | T -> DEL | LOC_Os11g44500.1 | N | frameshift_variant | Average:76.8; most accessible tissue: Minghui63 root, score: 88.829 | N | N | N | N |
| vg1126916922 | T -> C | LOC_Os11g44500.1 | synonymous_variant ; p.Asn143Asn; LOW | synonymous_codon | Average:76.8; most accessible tissue: Minghui63 root, score: 88.829 | N | N | N | N |
| vg1126916922 | T -> C | LOC_Os11g44500.1 | synonymous_variant ; p.Asn143Asn; LOW | nonsynonymous_codon | Average:76.8; most accessible tissue: Minghui63 root, score: 88.829 | benign  |
0.39 |
TOLERATED | 0.28 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1126916922 | NA | 8.79E-06 | mr1164 | Jap_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 |
| vg1126916922 | NA | 2.09E-06 | mr1548 | 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 |
| vg1126916922 | NA | 7.44E-08 | mr1010_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 |