Search for Variation information by Variation ID:
Detailed information for vg0815133904:
| Variant ID: vg0815133904 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 15133904 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.87, A: 0.14, others allele: 0.00, population size: 94. )
Flanking Sequence (100 bp) in Reference Genome:
GGTTGTGTGGGCTGTGTCACATGGGGTGCATCATCAGTTTGTGAAGTCCGAAGCTCATTGGGTACCGATGACAACCCTCCACTGAAGCTGGACATGTCGC[C/A]
GTACGATGCAGTGTAAGGTCTAAACCCTGACATTAGTTCAGGGCGAAATGACCCTACATAAGCAATGTAGATATCAATGAAATTATCAAAGCTGGAGCAA
Reverse complement sequence
TTGCTCCAGCTTTGATAATTTCATTGATATCTACATTGCTTATGTAGGGTCATTTCGCCCTGAACTAATGTCAGGGTTTAGACCTTACACTGCATCGTAC[G/T]
GCGACATGTCCAGCTTCAGTGGAGGGTTGTCATCGGTACCCAATGAGCTTCGGACTTCACAAACTGATGATGCACCCCATGTGACACAGCCCACACAACC
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 72.20% | 27.80% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 98.30% | 1.70% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 29.20% | 70.80% | 0.00% | 0.00% | NA |
| Aus | 269 | 55.80% | 44.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 96.30% | 3.20% | 0.43% | 0.00% | NA |
| Indica III | 913 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 97.50% | 2.50% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 14.20% | 85.80% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 53.80% | 46.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 25.30% | 74.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 58.30% | 41.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 57.80% | 42.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0815133904 | C -> A | LOC_Os08g24960.1 | missense_variant ; p.Gly58Cys; MODERATE | nonsynonymous_codon ; G58C | Average:36.79; most accessible tissue: Minghui63 root, score: 52.955 | benign  |
0.534 |
DELETERIOUS | 0.02 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0815133904 | NA | 7.20E-09 | mr1040 | 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 |
| vg0815133904 | NA | 2.47E-10 | mr1746 | 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 |
| vg0815133904 | NA | 7.59E-07 | mr1785 | 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 |
| vg0815133904 | 8.00E-07 | NA | mr1864 | 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 |
| vg0815133904 | NA | 1.08E-09 | mr1864 | 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 |