Search for Variation information by Variation ID:
Detailed information for vg0515921664:
| Variant ID: vg0515921664 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 15921664 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TGGTTCTGAATTGGCGAAAGCCCTCCGGTGCCGGCGCAGGGCGATTGCGCCGAACCGGAGACCCAAGATTGCTGTGGACGGCACCATGGAGGCGCGGTTC[G/A]
TTCTACTGCGGAAGGTTTGCTCCCGCCTTAGCTACCGTGACTTGGTGGAGGAATTTTGTATGCTTCGCATTTTTCCCATCTCCCAGTCATGGCAAGTCGC
Reverse complement sequence
GCGACTTGCCATGACTGGGAGATGGGAAAAATGCGAAGCATACAAAATTCCTCCACCAAGTCACGGTAGCTAAGGCGGGAGCAAACCTTCCGCAGTAGAA[C/T]
GAACCGCGCCTCCATGGTGCCGTCCACAGCAATCTTGGGTCTCCGGTTCGGCGCAATCGCCCTGCGCCGGCACCGGAGGGCTTTCGCCAATTCAGAACCA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 95.10% | 4.30% | 0.63% | 0.00% | NA |
| All Indica | 2759 | 91.70% | 7.20% | 1.09% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 85.90% | 12.90% | 1.18% | 0.00% | NA |
| Indica II | 465 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica III | 913 | 96.10% | 3.30% | 0.66% | 0.00% | NA |
| Indica Intermediate | 786 | 86.90% | 10.90% | 2.16% | 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 | 96.70% | 3.30% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0515921664 | G -> A | LOC_Os05g27390.1 | missense_variant ; p.Val192Ile; MODERATE | nonsynonymous_codon ; V192I | Average:41.09; most accessible tissue: Zhenshan97 flag leaf, score: 64.225 | benign  |
0.306 |
TOLERATED | 0.26 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0515921664 | 2.19E-06 | 2.19E-06 | mr1276_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 |