Search for Variation information by Variation ID:
Detailed information for vg1110902848:
| Variant ID: vg1110902848 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 10902848 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.80, T: 0.21, others allele: 0.00, population size: 222. )
Flanking Sequence (100 bp) in Reference Genome:
CCCGGCACTTTTCTGGACATCCTGACAAAACCATCAGTGAAAGAGGCAAACGACGAAGATAGCCCAGTCACCCCCGACATCAGCTCGGGGGCTACAGAGG[T/C]
AGAGCGCGCTGTTGCCGACATCGAGACCACGGATGACTGGCAGACCCCACTCATTAAATTCATAAGCAGCGACGAGTTGCCCAAGGACGACGGAGAAGCC
Reverse complement sequence
GGCTTCTCCGTCGTCCTTGGGCAACTCGTCGCTGCTTATGAATTTAATGAGTGGGGTCTGCCAGTCATCCGTGGTCTCGATGTCGGCAACAGCGCGCTCT[A/G]
CCTCTGTAGCCCCCGAGCTGATGTCGGGGGTGACTGGGCTATCTTCGTCGTTTGCCTCTTTCACTGATGGTTTTGTCAGGATGTCCAGAAAAGTGCCGGG
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 | 62.60% | 37.40% | 0.06% | 0.00% | NA |
| All Indica | 2759 | 93.50% | 6.50% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 2.80% | 97.20% | 0.07% | 0.00% | NA |
| Aus | 269 | 99.30% | 0.40% | 0.37% | 0.00% | NA |
| Indica I | 595 | 94.60% | 5.20% | 0.17% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 83.00% | 17.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 3.10% | 96.70% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 3.00% | 97.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 1.20% | 98.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 11.50% | 88.50% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 63.30% | 36.70% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1110902848 | T -> C | LOC_Os11g19110.1 | missense_variant ; p.Val1120Ala; MODERATE | nonsynonymous_codon ; V1120A | Average:43.238; most accessible tissue: Minghui63 young leaf, score: 61.887 | benign  |
-0.148 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1110902848 | NA | 2.56E-27 | mr1723 | 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 |
| vg1110902848 | 3.56E-06 | 6.65E-86 | mr1758 | 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 |
| vg1110902848 | 4.50E-06 | 4.50E-06 | mr1758 | 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 |
| vg1110902848 | NA | 1.51E-06 | mr1517_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 |
| vg1110902848 | NA | 2.04E-07 | mr1758_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 |
| vg1110902848 | NA | 9.01E-06 | mr1795_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 |