Search for Variation information by Variation ID:
Detailed information for vg0402649303:
| Variant ID: vg0402649303 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 2649303 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.90, G: 0.10, others allele: 0.00, population size: 39. )
Flanking Sequence (100 bp) in Reference Genome:
AAAGTAGTGTTGACGACGATCAAGCTGTTAAGGGCAGGCAACGGTCCGTCACGCTCCAGGACATCCATAGCTTGCCGCATAGAAGGGCGGTGTTGAGTCT[C/G]
CAAAGCAGAGCACCAGAGCCCCAATACGATGACACGCTCTATCTCTCTCATATCAAGGCCACCACCAATGGTTAACCTTGTATCCGCCGCCTCGACAACA
Reverse complement sequence
TGTTGTCGAGGCGGCGGATACAAGGTTAACCATTGGTGGTGGCCTTGATATGAGAGAGATAGAGCGTGTCATCGTATTGGGGCTCTGGTGCTCTGCTTTG[G/C]
AGACTCAACACCGCCCTTCTATGCGGCAAGCTATGGATGTCCTGGAGCGTGACGGACCGTTGCCTGCCCTTAACAGCTTGATCGTCGTCAACACTACTTT
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 29.70% | 26.60% | 13.06% | 30.60% | NA |
| All Indica | 2759 | 41.30% | 7.00% | 20.26% | 31.42% | NA |
| All Japonica | 1512 | 6.00% | 56.50% | 2.38% | 35.12% | NA |
| Aus | 269 | 35.30% | 53.20% | 4.09% | 7.43% | NA |
| Indica I | 595 | 48.10% | 4.00% | 38.49% | 9.41% | NA |
| Indica II | 465 | 41.10% | 15.90% | 13.98% | 29.03% | NA |
| Indica III | 913 | 44.60% | 2.40% | 12.16% | 40.85% | NA |
| Indica Intermediate | 786 | 32.40% | 9.40% | 19.59% | 38.55% | NA |
| Temperate Japonica | 767 | 1.30% | 85.70% | 1.83% | 11.21% | NA |
| Tropical Japonica | 504 | 12.70% | 24.00% | 3.37% | 59.92% | NA |
| Japonica Intermediate | 241 | 7.10% | 31.50% | 2.07% | 59.34% | NA |
| VI/Aromatic | 96 | 46.90% | 44.80% | 1.04% | 7.29% | NA |
| Intermediate | 90 | 38.90% | 26.70% | 11.11% | 23.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0402649303 | C -> DEL | LOC_Os04g05330.1 | N | frameshift_variant | Average:24.206; most accessible tissue: Callus, score: 47.712 | N | N | N | N |
| vg0402649303 | C -> G | LOC_Os04g05330.1 | missense_variant ; p.Glu582Gln; MODERATE | nonsynonymous_codon ; E582Q | Average:24.206; most accessible tissue: Callus, score: 47.712 | benign  |
0.982 |
TOLERATED | 0.26 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0402649303 | NA | 6.62E-06 | mr1280 | Jap_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 |
| vg0402649303 | 1.77E-06 | 1.76E-06 | mr1193_2 | Jap_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 |
| vg0402649303 | NA | 4.12E-07 | mr1521_2 | Jap_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 |