Search for Variation information by Variation ID:
Detailed information for vg0427967736:
| Variant ID: vg0427967736 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 27967736 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AGATTGGTGGGAAAATTACTGCAATGCACACCCTGAACCCACTAACATTGCTTGGGATGAGTTTGCTACGGCTTTCCGTACAGCTCATGTGCCTGAAAGC[G/A]
CTATTGATATGAAGAAAGAAGAATTCAACAGACTTAAGCAAGGCAACAGCAGTGTCAATGAGTACCTAAGTATGTTCAACAAGTTGGCTCGGTACGCCCC
Reverse complement sequence
GGGGCGTACCGAGCCAACTTGTTGAACATACTTAGGTACTCATTGACACTGCTGTTGCCTTGCTTAAGTCTGTTGAATTCTTCTTTCTTCATATCAATAG[C/T]
GCTTTCAGGCACATGAGCTGTACGGAAAGCCGTAGCAAACTCATCCCAAGCAATGTTAGTGGGTTCAGGGTGTGCATTGCAGTAATTTTCCCACCAATCT
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 | 53.90% | 0.10% | 12.87% | 33.09% | NA |
| All Indica | 2759 | 25.10% | 0.10% | 19.90% | 54.84% | NA |
| All Japonica | 1512 | 99.70% | 0.00% | 0.00% | 0.33% | NA |
| Aus | 269 | 69.10% | 0.00% | 20.07% | 10.78% | NA |
| Indica I | 595 | 20.80% | 0.20% | 12.10% | 66.89% | NA |
| Indica II | 465 | 12.90% | 0.00% | 24.73% | 62.37% | NA |
| Indica III | 913 | 31.30% | 0.00% | 23.44% | 45.24% | NA |
| Indica Intermediate | 786 | 28.40% | 0.40% | 18.83% | 52.42% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.00% | 0.26% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 74.40% | 1.10% | 5.56% | 18.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0427967736 | G -> DEL | LOC_Os04g47100.1 | N | frameshift_variant | Average:5.751; most accessible tissue: Minghui63 flag leaf, score: 9.254 | N | N | N | N |
| vg0427967736 | G -> A | LOC_Os04g47100.1 | missense_variant ; p.Ala506Thr; MODERATE | nonsynonymous_codon ; A506T | Average:5.751; most accessible tissue: Minghui63 flag leaf, score: 9.254 | benign  |
-0.139 |
TOLERATED | 0.51 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0427967736 | NA | 3.26E-09 | mr1827 | 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 |
| vg0427967736 | NA | 5.75E-06 | mr1467_2 | 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 |
| vg0427967736 | NA | 8.21E-06 | mr1759_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 |
| vg0427967736 | NA | 6.42E-06 | mr1873_2 | 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 |