Search for Variation information by Variation ID:
Detailed information for vg0321870228:
| Variant ID: vg0321870228 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 21870228 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 177. )
Flanking Sequence (100 bp) in Reference Genome:
TGGGGATGTGAGTTCTTTAGATTCTACTGGAATGAAGGGATGAGGTTGCCATCTATCGAAAACTGCCCTGGGTGCAGTGATATCGTCGAGAGCTCAAGCC[A/G]
GTCATATAATAGGGGTAATCGGCTGAGGCAGGCAAGAGTTTCTGTTAAACAAAGATTGGGTCCGGTGAATCAAGATCGTGGCCAAGAGGACGAGGTAATC
Reverse complement sequence
GATTACCTCGTCCTCTTGGCCACGATCTTGATTCACCGGACCCAATCTTTGTTTAACAGAAACTCTTGCCTGCCTCAGCCGATTACCCCTATTATATGAC[T/C]
GGCTTGAGCTCTCGACGATATCACTGCACCCAGGGCAGTTTTCGATAGATGGCAACCTCATCCCTTCATTCCAGTAGAATCTAAAGAACTCACATCCCCA
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 66.40% | 12.50% | 1.27% | 19.78% | NA |
| All Indica | 2759 | 52.90% | 13.40% | 2.17% | 31.50% | NA |
| All Japonica | 1512 | 98.30% | 0.00% | 0.00% | 1.65% | NA |
| Aus | 269 | 10.40% | 79.60% | 0.00% | 10.04% | NA |
| Indica I | 595 | 93.10% | 0.30% | 0.34% | 6.22% | NA |
| Indica II | 465 | 43.40% | 21.70% | 1.94% | 32.90% | NA |
| Indica III | 913 | 31.90% | 16.20% | 2.85% | 49.07% | NA |
| Indica Intermediate | 786 | 52.40% | 15.30% | 2.93% | 29.39% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 95.20% | 0.00% | 0.00% | 4.76% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 96.90% | 1.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 78.90% | 7.80% | 0.00% | 13.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0321870228 | A -> DEL | LOC_Os03g39350.1 | N | frameshift_variant | Average:40.196; most accessible tissue: Minghui63 flag leaf, score: 55.781 | N | N | N | N |
| vg0321870228 | A -> G | LOC_Os03g39350.1 | missense_variant ; p.Gln588Arg; MODERATE | nonsynonymous_codon ; Q588R | Average:40.196; most accessible tissue: Minghui63 flag leaf, score: 55.781 | benign  |
-0.383 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0321870228 | NA | 1.29E-07 | mr1425 | 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 |
| vg0321870228 | 8.98E-06 | 1.67E-06 | mr1425_2 | 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 |
| vg0321870228 | 1.42E-08 | 1.61E-11 | mr1425_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 |
| vg0321870228 | NA | 5.62E-06 | mr1629_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 |