Search for Variation information by Variation ID:
Detailed information for vg1200185437:
| Variant ID: vg1200185437 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 185437 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 68. )
Flanking Sequence (100 bp) in Reference Genome:
CAAAGTTTTCAGACAGCAGATCCAGTCAGCTATTGAGGGAGGCAAAATTAAATTTGATGATTCCAAGAGGCCGATGAAGGTTGATGGCAATCATTTTCCT[G/A]
TCAATATGGTGCACACATCTGGCCGAACAACCGATGGAGGAAGAGCTAGAGGCTTTCAGGTGAATTCGGCTAAGATTATCAATAAGTACCAGAAGAAATA
Reverse complement sequence
TATTTCTTCTGGTACTTATTGATAATCTTAGCCGAATTCACCTGAAAGCCTCTAGCTCTTCCTCCATCGGTTGTTCGGCCAGATGTGTGCACCATATTGA[C/T]
AGGAAAATGATTGCCATCAACCTTCATCGGCCTCTTGGAATCATCAAATTTAATTTTGCCTCCCTCAATAGCTGACTGGATCTGCTGTCTGAAAACTTTG
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 | 49.30% | 41.90% | 2.69% | 6.05% | NA |
| All Indica | 2759 | 20.70% | 68.40% | 3.23% | 7.68% | NA |
| All Japonica | 1512 | 96.30% | 0.30% | 0.53% | 2.91% | NA |
| Aus | 269 | 57.20% | 26.80% | 9.67% | 6.32% | NA |
| Indica I | 595 | 20.20% | 76.00% | 1.51% | 2.35% | NA |
| Indica II | 465 | 16.60% | 62.20% | 3.23% | 18.06% | NA |
| Indica III | 913 | 19.70% | 74.80% | 2.30% | 3.18% | NA |
| Indica Intermediate | 786 | 24.60% | 59.00% | 5.60% | 10.81% | NA |
| Temperate Japonica | 767 | 95.00% | 0.40% | 0.52% | 4.04% | NA |
| Tropical Japonica | 504 | 97.40% | 0.00% | 0.40% | 2.18% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.40% | 0.83% | 0.83% | NA |
| VI/Aromatic | 96 | 96.90% | 2.10% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 64.40% | 17.80% | 4.44% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1200185437 | G -> DEL | LOC_Os12g01320.1 | N | frameshift_variant | Average:25.806; most accessible tissue: Minghui63 panicle, score: 42.799 | N | N | N | N |
| vg1200185437 | G -> A | LOC_Os12g01320.1 | missense_variant ; p.Val1058Ile; MODERATE | nonsynonymous_codon ; V1058I | Average:25.806; most accessible tissue: Minghui63 panicle, score: 42.799 | benign  |
0.639 |
TOLERATED | 0.17 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1200185437 | NA | 4.87E-07 | mr1029 | 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 |
| vg1200185437 | NA | 6.87E-09 | mr1047 | 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 |
| vg1200185437 | NA | 4.50E-07 | mr1189 | 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 |
| vg1200185437 | NA | 7.92E-07 | mr1450 | 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 |
| vg1200185437 | NA | 2.82E-08 | mr1622 | 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 |
| vg1200185437 | NA | 4.92E-07 | mr1625 | 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 |
| vg1200185437 | NA | 3.29E-07 | mr1642 | 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 |
| vg1200185437 | NA | 6.37E-06 | mr1725 | 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 |
| vg1200185437 | NA | 4.68E-08 | mr1796 | 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 |
| vg1200185437 | NA | 1.31E-07 | mr1990 | 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 |