Search for Variation information by Variation ID:
Detailed information for vg0417328671:
| Variant ID: vg0417328671 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 17328671 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, T: 0.08, others allele: 0.00, population size: 36. )
Flanking Sequence (100 bp) in Reference Genome:
CACGTTTTGAATAGCAATGTTGGTATTGAAATGAGCTTATTCGCCATTAGCAACAACCTCAGGGTCAAAATCTTTCACCTCTCTTAGAAGTGTTGACATG[C/T]
TGTGGCACACGTGAAAACCACATTGGTCTCCGATCTGTTGTGCGCATGCGAACTTGGTGTCATGGTAAAGTTCGTCCTTGCCCTCCTTGTGCCTACCACC
Reverse complement sequence
GGTGGTAGGCACAAGGAGGGCAAGGACGAACTTTACCATGACACCAAGTTCGCATGCGCACAACAGATCGGAGACCAATGTGGTTTTCACGTGTGCCACA[G/A]
CATGTCAACACTTCTAAGAGAGGTGAAAGATTTTGACCCTGAGGTTGTTGCTAATGGCGAATAAGCTCATTTCAATACCAACATTGCTATTCAAAACGTG
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 85.00% | 5.80% | 4.74% | 4.42% | NA |
| All Indica | 2759 | 95.70% | 0.50% | 2.83% | 0.94% | NA |
| All Japonica | 1512 | 62.00% | 16.60% | 9.26% | 12.10% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 86.70% | 0.20% | 9.08% | 4.03% | NA |
| Indica II | 465 | 97.20% | 1.90% | 0.86% | 0.00% | NA |
| Indica III | 913 | 99.10% | 0.00% | 0.88% | 0.00% | NA |
| Indica Intermediate | 786 | 97.60% | 0.60% | 1.53% | 0.25% | NA |
| Temperate Japonica | 767 | 34.20% | 29.90% | 15.12% | 20.86% | NA |
| Tropical Japonica | 504 | 98.00% | 0.80% | 0.79% | 0.40% | NA |
| Japonica Intermediate | 241 | 75.50% | 7.50% | 8.30% | 8.71% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 85.60% | 10.00% | 4.44% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0417328671 | C -> DEL | LOC_Os04g29224.1 | N | frameshift_variant | Average:29.36; most accessible tissue: Zhenshan97 flag leaf, score: 42.807 | N | N | N | N |
| vg0417328671 | C -> T | LOC_Os04g29224.1 | missense_variant ; p.Ser984Asn; MODERATE | nonsynonymous_codon ; S984N | Average:29.36; most accessible tissue: Zhenshan97 flag leaf, score: 42.807 | benign  |
-1.207 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0417328671 | 7.22E-06 | NA | mr1060 | 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 |
| vg0417328671 | NA | 8.53E-06 | mr1180 | 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 |
| vg0417328671 | NA | 6.70E-06 | mr1503 | 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 |
| vg0417328671 | 5.76E-06 | NA | mr1521 | 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 |
| vg0417328671 | NA | 1.12E-08 | mr1521 | 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 |
| vg0417328671 | NA | 1.76E-06 | mr1576 | 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 |
| vg0417328671 | 5.81E-06 | NA | mr1648 | 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 |
| vg0417328671 | NA | 1.22E-06 | mr1748 | 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 |
| vg0417328671 | NA | 5.91E-07 | mr1783 | 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 |
| vg0417328671 | NA | 5.78E-06 | mr1788 | 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 |
| vg0417328671 | NA | 2.05E-06 | mr1880 | 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 |