Search for Variation information by Variation ID:
Detailed information for vg0301368204:
| Variant ID: vg0301368204 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 1368204 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TCAGCTGCCATCCGTACTTTGGTCTTTACGCACTACTCTCAGTCGGGCTACCGGACAGTCGCCGTTCTTTTTGGTTTATGGTGCAGAAGCTATGTTTCCA[T/A]
GTGAAGTGGAATTTGAATCACTACGATTTCAGAACTTCAACGAGGAGCGCTATGAAGAGGGCCGAGTTGACGACATCAATAGACTAGAAGAAGCCCGTGA
Reverse complement sequence
TCACGGGCTTCTTCTAGTCTATTGATGTCGTCAACTCGGCCCTCTTCATAGCGCTCCTCGTTGAAGTTCTGAAATCGTAGTGATTCAAATTCCACTTCAC[A/T]
TGGAAACATAGCTTCTGCACCATAAACCAAAAAGAACGGCGACTGTCCGGTAGCCCGACTGAGAGTAGTGCGTAAAGACCAAAGTACGGATGGCAGCTGA
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 36.40% | 9.70% | 1.95% | 51.99% | NA |
| All Indica | 2759 | 10.30% | 3.10% | 1.81% | 84.81% | NA |
| All Japonica | 1512 | 84.20% | 15.50% | 0.00% | 0.26% | NA |
| Aus | 269 | 44.60% | 25.70% | 14.13% | 15.61% | NA |
| Indica I | 595 | 4.20% | 7.60% | 1.51% | 86.72% | NA |
| Indica II | 465 | 15.30% | 0.90% | 1.51% | 82.37% | NA |
| Indica III | 913 | 11.30% | 0.30% | 1.86% | 86.53% | NA |
| Indica Intermediate | 786 | 10.70% | 4.30% | 2.16% | 82.82% | NA |
| Temperate Japonica | 767 | 94.50% | 5.30% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 69.40% | 30.20% | 0.00% | 0.40% | NA |
| Japonica Intermediate | 241 | 82.20% | 17.40% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 12.50% | 45.80% | 4.17% | 37.50% | NA |
| Intermediate | 90 | 35.60% | 25.60% | 0.00% | 38.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0301368204 | T -> A | LOC_Os03g03210.1 | missense_variant ; p.Cys932Ser; MODERATE | nonsynonymous_codon ; C932S | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
-0.782 |
TOLERATED | 1.00 |
| vg0301368204 | T -> DEL | LOC_Os03g03210.1 | 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 |
|---|---|---|---|---|---|---|
| vg0301368204 | 3.85E-06 | NA | mr1193_2 | 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 |