Search for Variation information by Variation ID:
Detailed information for vg0504038203:
| Variant ID: vg0504038203 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 4038203 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.89, T: 0.11, others allele: 0.00, population size: 200. )
Flanking Sequence (100 bp) in Reference Genome:
ACTGAAGAAAACAGATAATTTCCAATGGGGACCCGAAGCACAGAGGGCCTTCGAAGATTTCAAACAACTCCTCACCAAGCCACCGGTCTTAGCTTCACCA[C/T]
ACCCGCAGGAGCCGTTGTTGCTGTACGTATCAGCCACCTCCCAGGTCGTGAGCACAGTCCTGGTTGTCGAGCGTGAGGAAGAAGGCCATGTCCAGAAAGT
Reverse complement sequence
ACTTTCTGGACATGGCCTTCTTCCTCACGCTCGACAACCAGGACTGTGCTCACGACCTGGGAGGTGGCTGATACGTACAGCAACAACGGCTCCTGCGGGT[G/A]
TGGTGAAGCTAAGACCGGTGGCTTGGTGAGGAGTTGTTTGAAATCTTCGAAGGCCCTCTGTGCTTCGGGTCCCCATTGGAAATTATCTGTTTTCTTCAGT
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 | 84.90% | 1.20% | 6.90% | 7.00% | NA |
| All Indica | 2759 | 75.90% | 1.70% | 11.42% | 10.98% | NA |
| All Japonica | 1512 | 97.90% | 0.10% | 0.20% | 1.79% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 84.40% | 0.30% | 6.72% | 8.57% | NA |
| Indica II | 465 | 78.90% | 3.00% | 10.32% | 7.74% | NA |
| Indica III | 913 | 68.00% | 2.00% | 15.44% | 14.57% | NA |
| Indica Intermediate | 786 | 77.00% | 1.50% | 10.94% | 10.56% | NA |
| Temperate Japonica | 767 | 99.10% | 0.10% | 0.00% | 0.78% | NA |
| Tropical Japonica | 504 | 98.00% | 0.00% | 0.40% | 1.59% | NA |
| Japonica Intermediate | 241 | 93.80% | 0.40% | 0.41% | 5.39% | NA |
| VI/Aromatic | 96 | 89.60% | 7.30% | 3.12% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 0.00% | 4.44% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0504038203 | C -> T | LOC_Os05g07540.1 | missense_variant ; p.His1267Tyr; MODERATE | nonsynonymous_codon ; H1267Y | Average:11.77; most accessible tissue: Minghui63 panicle, score: 16.27 | benign  |
0.161 |
DELETERIOUS | 0.02 |
| vg0504038203 | C -> DEL | LOC_Os05g07540.1 | N | frameshift_variant | Average:11.77; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0504038203 | 7.85E-08 | 6.83E-08 | mr1006 | 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 |
| vg0504038203 | 1.78E-07 | 1.42E-07 | mr1007 | 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 |
| vg0504038203 | 2.37E-06 | NA | mr1051 | 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 |
| vg0504038203 | 1.03E-07 | 9.84E-08 | mr1052 | 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 |
| vg0504038203 | 6.06E-06 | 6.58E-06 | mr1006_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 |