Search for Variation information by Variation ID:
Detailed information for vg0314644181:
| Variant ID: vg0314644181 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 14644181 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GTGGCGGGTGGGCTGGGCGTTTGCTCGACCATGTCGAGGCTCCGCTTGTCGCATTGCACCACCAGCTTTGTATTCCCCTGAATAGTGATTGTTCCCTTCG[G/A]
TCCCGGCATCTTAAGCATTTGATATGCGTAGTGAGATGCGGCCATGAACTTCGCAAGTGCAGTTCTCCCGATGATGGCGTTGTAAGCTGTATCGAATTCA
Reverse complement sequence
TGAATTCGATACAGCTTACAACGCCATCATCGGGAGAACTGCACTTGCGAAGTTCATGGCCGCATCTCACTACGCATATCAAATGCTTAAGATGCCGGGA[C/T]
CGAAGGGAACAATCACTATTCAGGGGAATACAAAGCTGGTGGTGCAATGCGACAAGCGGAGCCTCGACATGGTCGAGCAAACGCCCAGCCCACCCGCCAC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 84.00% | 4.50% | 11.32% | 0.15% | NA |
| All Indica | 2759 | 74.90% | 6.90% | 17.91% | 0.25% | NA |
| All Japonica | 1512 | 99.50% | 0.20% | 0.26% | 0.00% | NA |
| Aus | 269 | 86.20% | 5.60% | 8.18% | 0.00% | NA |
| Indica I | 595 | 72.30% | 3.50% | 24.20% | 0.00% | NA |
| Indica II | 465 | 44.30% | 14.80% | 39.35% | 1.51% | NA |
| Indica III | 913 | 92.90% | 4.20% | 2.96% | 0.00% | NA |
| Indica Intermediate | 786 | 74.20% | 8.00% | 17.81% | 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 | 80.00% | 5.60% | 14.44% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0314644181 | G -> A | LOC_Os03g25590.1 | missense_variant ; p.Pro548Ser; MODERATE | nonsynonymous_codon ; P548S | Average:39.212; most accessible tissue: Minghui63 flag leaf, score: 71.577 | possibly damaging  |
1.822 |
DELETERIOUS | 0.02 |
| vg0314644181 | G -> DEL | LOC_Os03g25590.1 | N | frameshift_variant | Average:39.212; most accessible tissue: Minghui63 flag leaf, score: 71.577 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0314644181 | 4.43E-06 | NA | mr1542 | 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 |
| vg0314644181 | 3.80E-06 | 2.03E-14 | mr1542 | 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 |
| vg0314644181 | 5.62E-07 | NA | mr1542_2 | 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 |
| vg0314644181 | 5.29E-08 | 1.67E-18 | 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 |