Search for Variation information by Variation ID:
Detailed information for vg0404085688:
| Variant ID: vg0404085688 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 4085688 |
| Reference Allele: G | Alternative Allele: T,A |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GAGGCGAACCCCGAGAAAATCGATGCCATTCAGCAAATGAAGCCCCCATCGAGCGTACGCGAAGTACAAAAGCTCGCAGGCCAAATTGCGGCGCTCAGTC[G/T,A]
ATTCCTCTCAAAGGCAGCCGAAAGAGGTTTGCCCTTCTTCAAGACCCTCCGGGGCGCGGGAAAGTTTAGCTGGACACCCGAATGCCAAGCAGCGTTCGAC
Reverse complement sequence
GTCGAACGCTGCTTGGCATTCGGGTGTCCAGCTAAACTTTCCCGCGCCCCGGAGGGTCTTGAAGAAGGGCAAACCTCTTTCGGCTGCCTTTGAGAGGAAT[C/A,T]
GACTGAGCGCCGCAATTTGGCCTGCGAGCTTTTGTACTTCGCGTACGCTCGATGGGGGCTTCATTTGCTGAATGGCATCGATTTTCTCGGGGTTCGCCTC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 92.00% | 0.80% | 2.54% | 4.51% | A: 0.15% |
| All Indica | 2759 | 89.00% | 1.30% | 3.88% | 5.65% | A: 0.22% |
| All Japonica | 1512 | 96.20% | 0.00% | 0.53% | 3.31% | NA |
| Aus | 269 | 95.90% | 0.00% | 1.49% | 2.23% | A: 0.37% |
| Indica I | 595 | 81.80% | 3.20% | 5.71% | 9.24% | NA |
| Indica II | 465 | 88.60% | 1.10% | 5.81% | 4.09% | A: 0.43% |
| Indica III | 913 | 93.50% | 0.00% | 1.97% | 4.27% | A: 0.22% |
| Indica Intermediate | 786 | 89.30% | 1.40% | 3.56% | 5.47% | A: 0.25% |
| Temperate Japonica | 767 | 99.50% | 0.00% | 0.13% | 0.39% | NA |
| Tropical Japonica | 504 | 93.30% | 0.00% | 0.99% | 5.75% | NA |
| Japonica Intermediate | 241 | 91.70% | 0.00% | 0.83% | 7.47% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 1.10% | 1.11% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0404085688 | G -> DEL | LOC_Os04g07670.1 | N | frameshift_variant | Average:46.64; most accessible tissue: Minghui63 young leaf, score: 75.479 | N | N | N | N |
| vg0404085688 | G -> A | LOC_Os04g07670.1 | missense_variant ; p.Arg766Gln; MODERATE | nonsynonymous_codon ; R766Q | Average:46.64; most accessible tissue: Minghui63 young leaf, score: 75.479 | benign  |
1.077 |
DELETERIOUS | 0.02 |
| vg0404085688 | G -> T | LOC_Os04g07670.1 | missense_variant ; p.Arg766Leu; MODERATE | nonsynonymous_codon ; R766L | Average:46.64; most accessible tissue: Minghui63 young leaf, score: 75.479 | possibly damaging |
1.982 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0404085688 | 9.81E-06 | NA | mr1580 | 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 |