Search for Variation information by Variation ID:
Detailed information for vg0618997817:
| Variant ID: vg0618997817 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 18997817 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.66, T: 0.35, others allele: 0.00, population size: 222. )
Flanking Sequence (100 bp) in Reference Genome:
AATACCCTCTGTCACCTGGAGATGTTTTTCCCACTGTCTTTCTTTGATATAATGGTTCATCTCCCTGTTCATCTGGTGAAGCAAACAAAACTATGTGGCC[T/C]
GGCTTTTCTAAGGGAAATGTGGCCGTTTGAAAGGTACATGGGAGTTCTGAAGTCGTACGTTCGTAACAGAGCCAAACCCGAGGAGAGCATCATTGAAGGT
Reverse complement sequence
ACCTTCAATGATGCTCTCCTCGGGTTTGGCTCTGTTACGAACGTACGACTTCAGAACTCCCATGTACCTTTCAAACGGCCACATTTCCCTTAGAAAAGCC[A/G]
GGCCACATAGTTTTGTTTGCTTCACCAGATGAACAGGGAGATGAACCATTATATCAAAGAAAGACAGTGGGAAAAACATCTCCAGGTGACAGAGGGTATT
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 | 67.80% | 30.20% | 0.19% | 1.84% | NA |
| All Indica | 2759 | 97.00% | 2.80% | 0.14% | 0.07% | NA |
| All Japonica | 1512 | 7.40% | 87.10% | 0.33% | 5.16% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.80% | 1.50% | 0.50% | 0.17% | NA |
| Indica II | 465 | 95.90% | 4.10% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 94.50% | 5.20% | 0.13% | 0.13% | NA |
| Temperate Japonica | 767 | 4.60% | 88.80% | 0.13% | 6.52% | NA |
| Tropical Japonica | 504 | 12.70% | 85.50% | 0.20% | 1.59% | NA |
| Japonica Intermediate | 241 | 5.40% | 85.10% | 1.24% | 8.30% | NA |
| VI/Aromatic | 96 | 94.80% | 1.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 64.40% | 32.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0618997817 | T -> C | LOC_Os06g32660.1 | missense_variant ; p.Leu483Pro; MODERATE | nonsynonymous_codon ; L483P | Average:23.335; most accessible tissue: Minghui63 young leaf, score: 31.294 | benign  |
-0.984 |
TOLERATED | 1.00 |
| vg0618997817 | T -> DEL | LOC_Os06g32660.1 | N | frameshift_variant | Average:23.335; most accessible tissue: Minghui63 young leaf, score: 31.294 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0618997817 | NA | 1.62E-11 | mr1172 | 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 |
| vg0618997817 | NA | 5.26E-07 | mr1245 | 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 |
| vg0618997817 | NA | 1.07E-07 | mr1354 | 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 |
| vg0618997817 | 1.01E-06 | NA | mr1100_2 | Ind_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 |