Search for Variation information by Variation ID:
Detailed information for vg1122195808:
| Variant ID: vg1122195808 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 22195808 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.60, T: 0.39, others allele: 0.00, population size: 81. )
Flanking Sequence (100 bp) in Reference Genome:
GTCAGTATGGTGTACTGGCGCAGAACAAGGGCACGCGGAGATCATGAGAGCTTTGTCCCAGATTCGGAGAAAGAGATGCTGTGGACCACAATGCTCGAGA[T/C]
ATTCACCCTTCCCGCGGGTACAGAGGACAAAGTGAAAAGGTGGACTCTGAAGAAAATGGCAGAACAGTTTCAGAGCTTCAAGGGAGATCTGTACCAGAAA
Reverse complement sequence
TTTCTGGTACAGATCTCCCTTGAAGCTCTGAAACTGTTCTGCCATTTTCTTCAGAGTCCACCTTTTCACTTTGTCCTCTGTACCCGCGGGAAGGGTGAAT[A/G]
TCTCGAGCATTGTGGTCCACAGCATCTCTTTCTCCGAATCTGGGACAAAGCTCTCATGATCTCCGCGTGCCCTTGTTCTGCGCCAGTACACCATACTGAC
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 45.50% | 20.80% | 19.45% | 14.26% | NA |
| All Indica | 2759 | 41.00% | 21.50% | 23.34% | 14.24% | NA |
| All Japonica | 1512 | 50.60% | 24.50% | 10.78% | 14.09% | NA |
| Aus | 269 | 66.50% | 1.50% | 27.88% | 4.09% | NA |
| Indica I | 595 | 26.20% | 30.60% | 28.91% | 14.29% | NA |
| Indica II | 465 | 41.30% | 1.90% | 32.90% | 23.87% | NA |
| Indica III | 913 | 51.50% | 26.80% | 14.35% | 7.34% | NA |
| Indica Intermediate | 786 | 39.70% | 19.80% | 23.92% | 16.54% | NA |
| Temperate Japonica | 767 | 72.60% | 8.10% | 5.35% | 13.95% | NA |
| Tropical Japonica | 504 | 22.00% | 42.30% | 20.04% | 15.67% | NA |
| Japonica Intermediate | 241 | 40.20% | 39.80% | 8.71% | 11.20% | NA |
| VI/Aromatic | 96 | 34.40% | 2.10% | 19.79% | 43.75% | NA |
| Intermediate | 90 | 47.80% | 15.60% | 20.00% | 16.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1122195808 | T -> DEL | LOC_Os11g37600.1 | N | frameshift_variant | Average:14.888; most accessible tissue: Minghui63 root, score: 27.443 | N | N | N | N |
| vg1122195808 | T -> C | LOC_Os11g37600.1 | missense_variant ; p.Ile159Thr; MODERATE | nonsynonymous_codon ; I159T | Average:14.888; most accessible tissue: Minghui63 root, score: 27.443 | probably damaging  |
-2.188 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1122195808 | 2.07E-06 | 2.07E-06 | mr1146_2 | 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 |
| vg1122195808 | NA | 1.29E-06 | mr1222_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 |
| vg1122195808 | NA | 5.31E-06 | mr1929_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 |