Search for Variation information by Variation ID:
Detailed information for vg0314644172:
| Variant ID: vg0314644172 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 14644172 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGCTCAGTCGTGGCGGGTGGGCTGGGCGTTTGCTCGACCATGTCGAGGCTCCGCTTGTCGCATTGCACCACCAGCTTTGTATTCCCCTGAATAGTGATTG[T/G]
TCCCTTCGGTCCCGGCATCTTAAGCATTTGATATGCGTAGTGAGATGCGGCCATGAACTTCGCAAGTGCAGTTCTCCCGATGATGGCGTTGTAAGCTGTA
Reverse complement sequence
TACAGCTTACAACGCCATCATCGGGAGAACTGCACTTGCGAAGTTCATGGCCGCATCTCACTACGCATATCAAATGCTTAAGATGCCGGGACCGAAGGGA[A/C]
CAATCACTATTCAGGGGAATACAAAGCTGGTGGTGCAATGCGACAAGCGGAGCCTCGACATGGTCGAGCAAACGCCCAGCCCACCCGCCACGACTGAGCC
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 84.50% | 4.50% | 10.96% | 0.04% | NA |
| All Indica | 2759 | 75.70% | 6.70% | 17.47% | 0.07% | NA |
| All Japonica | 1512 | 99.50% | 0.20% | 0.26% | 0.00% | NA |
| Aus | 269 | 86.60% | 6.70% | 6.69% | 0.00% | NA |
| Indica I | 595 | 72.80% | 3.40% | 23.87% | 0.00% | NA |
| Indica II | 465 | 47.30% | 14.20% | 38.06% | 0.43% | NA |
| Indica III | 913 | 93.00% | 4.20% | 2.85% | 0.00% | NA |
| Indica Intermediate | 786 | 74.70% | 7.90% | 17.43% | 0.00% | NA |
| Temperate Japonica | 767 | 99.70% | 0.10% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.40% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 96.90% | 1.00% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 81.10% | 5.60% | 13.33% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0314644172 | T -> DEL | LOC_Os03g25590.1 | N | frameshift_variant | Average:39.096; most accessible tissue: Minghui63 flag leaf, score: 72.907 | N | N | N | N |
| vg0314644172 | T -> G | LOC_Os03g25590.1 | missense_variant ; p.Thr551Pro; MODERATE | nonsynonymous_codon ; T551P | Average:39.096; most accessible tissue: Minghui63 flag leaf, score: 72.907 | probably damaging  |
2.085 |
TOLERATED | 0.37 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0314644172 | 9.19E-07 | NA | mr1542 | 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 |
| vg0314644172 | 2.53E-06 | 1.70E-15 | mr1542 | 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 |
| vg0314644172 | 3.88E-07 | NA | mr1542_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 |
| vg0314644172 | 2.01E-07 | 5.70E-19 | mr1542_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 |