Search for Variation information by Variation ID:
Detailed information for vg1128009892:
| Variant ID: vg1128009892 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 28009892 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 336. )
Flanking Sequence (100 bp) in Reference Genome:
ATTCCTGTTACTTCTGTTTCAGGTCTTACTGTGGGAAGTATAATGCTTGGGGATATTTCATTCATATCAGTGAACCAGGTGGGGGCTACAGCTGCCAGGG[T/A]
AATACATGATACCAAAAATACCCACTCAAGGACGACTACAATTCAGCAGCCAAGCAAGAAAGAACAGCCTGAGGAAGGTGCTCTGAACAACATGGCAGTA
Reverse complement sequence
TACTGCCATGTTGTTCAGAGCACCTTCCTCAGGCTGTTCTTTCTTGCTTGGCTGCTGAATTGTAGTCGTCCTTGAGTGGGTATTTTTGGTATCATGTATT[A/T]
CCCTGGCAGCTGTAGCCCCCACCTGGTTCACTGATATGAATGAAATATCCCCAAGCATTATACTTCCCACAGTAAGACCTGAAACAGAAGTAACAGGAAT
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 88.90% | 11.00% | 0.08% | 0.00% | NA |
| All Indica | 2759 | 98.80% | 1.10% | 0.14% | 0.00% | NA |
| All Japonica | 1512 | 75.80% | 24.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 59.90% | 40.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.70% | 1.20% | 0.17% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.70% | 0.20% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 97.70% | 2.00% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 84.50% | 15.50% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 65.90% | 34.10% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 68.90% | 31.10% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 81.10% | 18.90% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1128009892 | T -> A | LOC_Os11g46250.1 | missense_variant ; p.Val790Glu; MODERATE | nonsynonymous_codon ; V790E | Average:61.242; most accessible tissue: Zhenshan97 root, score: 83.907 | benign  |
-1.439 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1128009892 | NA | 1.22E-06 | mr1345 | 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 |
| vg1128009892 | 3.44E-06 | NA | mr1345 | 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 |
| vg1128009892 | NA | 9.65E-06 | mr1353 | 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 |
| vg1128009892 | 6.21E-06 | 6.21E-06 | mr1459 | 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 |
| vg1128009892 | 7.68E-07 | 3.84E-06 | mr1604 | 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 |
| vg1128009892 | 1.70E-07 | NA | mr1745 | 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 |