Search for Variation information by Variation ID:
Detailed information for vg0819130178:
| Variant ID: vg0819130178 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 19130178 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 291. )
Flanking Sequence (100 bp) in Reference Genome:
GCCGCCATCCAAGACGGAGGTGGAGCCATCTAATGTGATACCTATCACATTGGATGATTTCGAAGGGGAAGACCGCAAGTCCATGGAGGAGTACATCAAG[G/A]
AGATCACACAGGAGGCGCTGATGAGAGCATGCACTAGGACTCGTCAAGGCGTGATCATCAAGCCCAGGCCACGTCCTAAGCTCGCTTCTGATTTGGTAAG
Reverse complement sequence
CTTACCAAATCAGAAGCGAGCTTAGGACGTGGCCTGGGCTTGATGATCACGCCTTGACGAGTCCTAGTGCATGCTCTCATCAGCGCCTCCTGTGTGATCT[C/T]
CTTGATGTACTCCTCCATGGACTTGCGGTCTTCCCCTTCGAAATCATCCAATGTGATAGGTATCACATTAGATGGCTCCACCTCCGTCTTGGATGGCGGC
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 | 96.10% | 3.90% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 93.00% | 7.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 89.80% | 10.20% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 88.80% | 11.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 49.00% | 51.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0819130178 | G -> A | LOC_Os08g30990.1 | missense_variant ; p.Glu37Lys; MODERATE | nonsynonymous_codon ; E37K | Average:43.623; most accessible tissue: Minghui63 flag leaf, score: 56.489 | benign  |
0.481 |
TOLERATED | 0.09 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0819130178 | 8.88E-06 | 8.88E-06 | mr1038 | 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 |
| vg0819130178 | 2.34E-07 | 2.34E-07 | mr1389 | 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 |
| vg0819130178 | 3.20E-10 | 3.06E-11 | mr1038_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 |
| vg0819130178 | 2.58E-09 | 2.58E-09 | mr1389_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 |