Search for Variation information by Variation ID:
Detailed information for vg0800337100:
| Variant ID: vg0800337100 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 337100 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 286. )
Flanking Sequence (100 bp) in Reference Genome:
AATTTCTACCTTTTAACATTTCCCATGGACAAATTGATGGAACTAAATATATCTATTACCTTGTGGAATACGAAGGCCATTTTCACGTTCCAATGCATCT[C/T]
TTAAAACTACAGCATCATGTGCTGTCCCCTCCCAACCAACCAAGACATAAGTGAACCGAAGATCAAAATCTACGGCCGCCATTACATTTTGCGTGGCATG
Reverse complement sequence
CATGCCACGCAAAATGTAATGGCGGCCGTAGATTTTGATCTTCGGTTCACTTATGTCTTGGTTGGTTGGGAGGGGACAGCACATGATGCTGTAGTTTTAA[G/A]
AGATGCATTGGAACGTGAAAATGGCCTTCGTATTCCACAAGGTAATAGATATATTTAGTTCCATCAATTTGTCCATGGGAAATGTTAAAAGGTAGAAATT
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 | 89.40% | 3.40% | 1.14% | 6.09% | NA |
| All Indica | 2759 | 86.80% | 4.80% | 1.23% | 7.18% | NA |
| All Japonica | 1512 | 97.50% | 0.20% | 0.86% | 1.46% | NA |
| Aus | 269 | 82.90% | 0.00% | 1.49% | 15.61% | NA |
| Indica I | 595 | 98.70% | 0.20% | 0.50% | 0.67% | NA |
| Indica II | 465 | 63.20% | 18.10% | 3.66% | 15.05% | NA |
| Indica III | 913 | 91.80% | 0.90% | 0.77% | 6.57% | NA |
| Indica Intermediate | 786 | 85.90% | 5.10% | 0.89% | 8.14% | NA |
| Temperate Japonica | 767 | 99.10% | 0.10% | 0.13% | 0.65% | NA |
| Tropical Japonica | 504 | 95.80% | 0.40% | 1.59% | 2.18% | NA |
| Japonica Intermediate | 241 | 95.90% | 0.00% | 1.66% | 2.49% | NA |
| VI/Aromatic | 96 | 58.30% | 19.80% | 1.04% | 20.83% | NA |
| Intermediate | 90 | 85.60% | 5.60% | 2.22% | 6.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0800337100 | C -> T | LOC_Os08g01570.1 | missense_variant ; p.Arg212Lys; MODERATE | nonsynonymous_codon ; R212K | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
1.032 |
TOLERATED | 0.77 |
| vg0800337100 | C -> DEL | LOC_Os08g01570.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0800337100 | NA | 7.25E-07 | mr1193 | 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 |
| vg0800337100 | NA | 4.21E-06 | mr1193 | 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 |
| vg0800337100 | 2.48E-07 | 3.20E-09 | mr1197 | 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 |
| vg0800337100 | 6.54E-06 | 6.54E-06 | mr1197 | 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 |
| vg0800337100 | NA | 1.63E-06 | mr1193_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 |