Search for Variation information by Variation ID:
Detailed information for vg0301371527:
| Variant ID: vg0301371527 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 1371527 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TTGCTCTTGTTTGGCTGAGGCTTAAGGAAGAAGATACGGCGGAACAAGGCAAAATGAGGCCTAATGCCCAGAAAAGCTTCGCAGACGTGAATAAAATTGG[C/T]
AATATGCACTATGGAGTTTGGATTCAGATGATGCAGGCTGATTCCGTAGAAATTCAAAATTCCCCGAAAAAATCTTGAGGTTGGAAGGGAGAAACCGCCA
Reverse complement sequence
TGGCGGTTTCTCCCTTCCAACCTCAAGATTTTTTCGGGGAATTTTGAATTTCTACGGAATCAGCCTGCATCATCTGAATCCAAACTCCATAGTGCATATT[G/A]
CCAATTTTATTCACGTCTGCGAAGCTTTTCTGGGCATTAGGCCTCATTTTGCCTTGTTCCGCCGTATCTTCTTCCTTAAGCCTCAGCCAAACAAGAGCAA
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 | 84.80% | 8.90% | 4.32% | 1.95% | NA |
| All Indica | 2759 | 80.60% | 9.90% | 6.89% | 2.54% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Aus | 269 | 50.90% | 47.20% | 1.12% | 0.74% | NA |
| Indica I | 595 | 94.60% | 0.80% | 4.37% | 0.17% | NA |
| Indica II | 465 | 75.50% | 10.50% | 10.32% | 3.66% | NA |
| Indica III | 913 | 73.70% | 15.60% | 6.90% | 3.83% | NA |
| Indica Intermediate | 786 | 81.20% | 9.90% | 6.74% | 2.16% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 66.70% | 14.60% | 2.08% | 16.67% | NA |
| Intermediate | 90 | 82.20% | 5.60% | 7.78% | 4.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0301371527 | C -> T | LOC_Os03g03220.1 | missense_variant ; p.Ala97Thr; MODERATE | nonsynonymous_codon ; A97T | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
0.729 |
DELETERIOUS | 0.02 |
| vg0301371527 | C -> DEL | LOC_Os03g03220.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0301371527 | NA | 9.40E-06 | mr1295 | 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 |
| vg0301371527 | NA | 1.42E-06 | mr1708 | 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 |