Search for Variation information by Variation ID:
Detailed information for vg0200442960:
| Variant ID: vg0200442960 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 442960 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTACCTGAACTTGAGCATCAACTCTCTTGAAGGCCGTATTCCAGATGAGCTGTCCTCATGCAGCAATCTCCAGGTACTCGGCTTATCGAACAACTCCTTC[G/C]
AAGGTGAGATACCACCAAGCTTAACCCAATGCACTCGCCTCCAGCAAGTTATACTATACAACAACAAGCTTGAAGGCAGTATACCCACCAGATTTGGAAC
Reverse complement sequence
GTTCCAAATCTGGTGGGTATACTGCCTTCAAGCTTGTTGTTGTATAGTATAACTTGCTGGAGGCGAGTGCATTGGGTTAAGCTTGGTGGTATCTCACCTT[C/G]
GAAGGAGTTGTTCGATAAGCCGAGTACCTGGAGATTGCTGCATGAGGACAGCTCATCTGGAATACGGCCTTCAAGAGAGTTGATGCTCAAGTTCAGGTAG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.60% | 0.10% | 0.32% | 0.00% | NA |
| All Indica | 2759 | 99.70% | 0.10% | 0.18% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 95.20% | 1.10% | 3.72% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.70% | 0.10% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 99.50% | 0.10% | 0.38% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0200442960 | G -> C | LOC_Os02g01800.1 | missense_variant ; p.Glu214Gln; MODERATE | nonsynonymous_codon ; E214Q | Average:65.66; most accessible tissue: Zhenshan97 root, score: 85.912 | benign  |
0.28 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0200442960 | 3.81E-06 | NA | mr1748_2 | 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 |