Search for Variation information by Variation ID:
Detailed information for vg0526442423:
| Variant ID: vg0526442423 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 26442423 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CCACGCCACGCGATCAAGAGCCAGGCCCTCGCCGACTTTGTGGCAGAGTGGACCCCAGCTCCCGAGCCCGTCTCCGTCCCCGAGGCCAGCTCGGGCCCCT[C/T]
GCAGCTGCCTCACACCGCCTACTGGGTGATGCAGTTCAACGGGTCCTTGTCTCTTCAGGGTGCCGGTGCGGGAGTCACATTGACCTCACCGAGCGGAGAC
Reverse complement sequence
GTCTCCGCTCGGTGAGGTCAATGTGACTCCCGCACCGGCACCCTGAAGAGACAAGGACCCGTTGAACTGCATCACCCAGTAGGCGGTGTGAGGCAGCTGC[G/A]
AGGGGCCCGAGCTGGCCTCGGGGACGGAGACGGGCTCGGGAGCTGGGGTCCACTCTGCCACAAAGTCGGCGAGGGCCTGGCTCTTGATCGCGTGGCGTGG
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 | 56.90% | 0.10% | 2.48% | 40.52% | NA |
| All Indica | 2759 | 37.50% | 0.10% | 2.65% | 59.66% | NA |
| All Japonica | 1512 | 93.70% | 0.00% | 0.13% | 6.15% | NA |
| Aus | 269 | 46.80% | 0.00% | 10.78% | 42.38% | NA |
| Indica I | 595 | 17.60% | 0.00% | 2.18% | 80.17% | NA |
| Indica II | 465 | 48.20% | 0.00% | 2.15% | 49.68% | NA |
| Indica III | 913 | 47.00% | 0.40% | 2.63% | 49.95% | NA |
| Indica Intermediate | 786 | 35.40% | 0.00% | 3.31% | 61.32% | NA |
| Temperate Japonica | 767 | 97.10% | 0.00% | 0.13% | 2.74% | NA |
| Tropical Japonica | 504 | 95.00% | 0.00% | 0.20% | 4.76% | NA |
| Japonica Intermediate | 241 | 80.10% | 0.00% | 0.00% | 19.92% | NA |
| VI/Aromatic | 96 | 46.90% | 0.00% | 11.46% | 41.67% | NA |
| Intermediate | 90 | 73.30% | 0.00% | 2.22% | 24.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0526442423 | C -> T | LOC_Os05g45620.1 | missense_variant ; p.Ser1323Leu; MODERATE | nonsynonymous_codon ; S1323L | Average:41.621; most accessible tissue: Minghui63 root, score: 77.565 | benign  |
0.457 |
DELETERIOUS | 0.00 |
| vg0526442423 | C -> DEL | LOC_Os05g45620.1 | N | frameshift_variant | Average:41.621; most accessible tissue: Minghui63 root, score: 77.565 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0526442423 | 4.60E-06 | 4.26E-07 | mr1053 | 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 |
| vg0526442423 | 8.98E-06 | 8.98E-06 | mr1258 | 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 |
| vg0526442423 | NA | 7.50E-06 | mr1963 | 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 |