Search for Variation information by Variation ID:
Detailed information for vg0619684836:
| Variant ID: vg0619684836 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 19684836 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AACCAGGAGGGGAACGTGGAGAGGGATGCGGAGGGGAACGAGGAGGAGGAGGCTAGTGCAAGTCAACCCTCCACTGGACAGAAGAGGGCACGCGGGCAAC[G/A]
AGGTGCCGCGAAGAAGATAGAGGGTCGGCACATCATAACGGAAGTGGTCGAAGACGGCCGACCTAGTGCCCCGGCAGAAGCAGCCAAGAACTACGTACGA
Reverse complement sequence
TCGTACGTAGTTCTTGGCTGCTTCTGCCGGGGCACTAGGTCGGCCGTCTTCGACCACTTCCGTTATGATGTGCCGACCCTCTATCTTCTTCGCGGCACCT[C/T]
GTTGCCCGCGTGCCCTCTTCTGTCCAGTGGAGGGTTGACTTGCACTAGCCTCCTCCTCCTCGTTCCCCTCCGCATCCCTCTCCACGTTCCCCTCCTGGTT
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 | 92.60% | 5.60% | 0.21% | 1.63% | NA |
| All Indica | 2759 | 99.20% | 0.70% | 0.00% | 0.07% | NA |
| All Japonica | 1512 | 83.70% | 16.10% | 0.07% | 0.13% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.00% | 2.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.00% | 0.00% | 0.11% | NA |
| Indica Intermediate | 786 | 99.00% | 0.90% | 0.00% | 0.13% | NA |
| Temperate Japonica | 767 | 76.00% | 23.90% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 93.80% | 6.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 87.10% | 12.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 18.80% | 1.00% | 7.29% | 72.92% | NA |
| Intermediate | 90 | 92.20% | 2.20% | 2.22% | 3.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0619684836 | G -> A | LOC_Os06g33830.1 | missense_variant ; p.Arg81Gln; MODERATE | nonsynonymous_codon ; R81Q | Average:60.26; most accessible tissue: Zhenshan97 flag leaf, score: 76.356 | benign  |
0.765 |
DELETERIOUS | 0.03 |
| vg0619684836 | G -> DEL | LOC_Os06g33830.1 | N | frameshift_variant | Average:60.26; most accessible tissue: Zhenshan97 flag leaf, score: 76.356 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0619684836 | NA | 5.81E-06 | mr1884 | 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 |
| vg0619684836 | 8.88E-07 | 2.37E-07 | mr1456_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 |
| vg0619684836 | 2.60E-06 | 9.57E-09 | mr1456_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 |
| vg0619684836 | NA | 9.22E-06 | mr1792_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 |