Search for Variation information by Variation ID:
Detailed information for vg1124422531:
| Variant ID: vg1124422531 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 24422531 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, T: 0.03, others allele: 0.00, population size: 195. )
Flanking Sequence (100 bp) in Reference Genome:
TGGAGATAATCCAAGGCAGCAGCAATGTCCGTTGCTATCTGTATAATTGATCCTAGACCTAATGGTCTTCTTTGTCGATGTTTTTGTACTTTTGGATGAA[G/T]
CCAACTTTCTAGGTTACCATTAGCCATGTACTCCAAAATTAGAGCTTTAAACTCTTTTCCCATTGGATCGAAGGAGGAACATAGACTAATCACATGCATG
Reverse complement sequence
CATGCATGTGATTAGTCTATGTTCCTCCTTCGATCCAATGGGAAAAGAGTTTAAAGCTCTAATTTTGGAGTACATGGCTAATGGTAACCTAGAAAGTTGG[C/A]
TTCATCCAAAAGTACAAAAACATCGACAAAGAAGACCATTAGGTCTAGGATCAATTATACAGATAGCAACGGACATTGCTGCTGCCTTGGATTATCTCCA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 68.50% | 31.10% | 0.13% | 0.34% | NA |
| All Indica | 2759 | 60.40% | 38.90% | 0.14% | 0.54% | NA |
| All Japonica | 1512 | 89.20% | 10.80% | 0.00% | 0.07% | NA |
| Aus | 269 | 51.70% | 48.30% | 0.00% | 0.00% | NA |
| Indica I | 595 | 74.60% | 25.00% | 0.00% | 0.34% | NA |
| Indica II | 465 | 53.50% | 44.90% | 0.22% | 1.29% | NA |
| Indica III | 913 | 58.10% | 41.60% | 0.11% | 0.22% | NA |
| Indica Intermediate | 786 | 56.40% | 42.70% | 0.25% | 0.64% | NA |
| Temperate Japonica | 767 | 96.30% | 3.70% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 80.60% | 19.20% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 84.20% | 15.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 17.70% | 82.30% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 73.30% | 24.40% | 2.22% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1124422531 | G -> T | LOC_Os11g40810.1 | missense_variant ; p.Leu518Ile; MODERATE | nonsynonymous_codon ; L518I | Average:45.206; most accessible tissue: Callus, score: 72.95 | benign  |
0.568 |
TOLERATED | 0.24 |
| vg1124422531 | G -> DEL | LOC_Os11g40810.1 | N | frameshift_variant | Average:45.206; most accessible tissue: Callus, score: 72.95 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1124422531 | NA | 3.29E-06 | mr1309 | 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 |
| vg1124422531 | 1.34E-09 | 1.34E-09 | mr1855 | 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 |
| vg1124422531 | NA | 9.10E-06 | mr1238_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 |
| vg1124422531 | NA | 6.38E-08 | mr1609_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 |
| vg1124422531 | NA | 6.83E-06 | mr1900_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 |