Search for Variation information by Variation ID:
Detailed information for vg0519671296:
| Variant ID: vg0519671296 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 19671296 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TCGGAGGACATAGTCACTGATCGAAAGTATGCGTGCTCGGATGCGCTTCTCATGATAACGGCGGAGGGCTTGTTGATAGCTAGCTGCTCGAACGGCAACT[C/T]
GCTCACGATGCTCCTCGAGAAGGTTTACATCGATGTCTCGCTGTTCCTCCTGGTTCTCGTCGGAATGCTTCTGTACTCGTGTACTTTGATGTCGTAACTC
Reverse complement sequence
GAGTTACGACATCAAAGTACACGAGTACAGAAGCATTCCGACGAGAACCAGGAGGAACAGCGAGACATCGATGTAAACCTTCTCGAGGAGCATCGTGAGC[G/A]
AGTTGCCGTTCGAGCAGCTAGCTATCAACAAGCCCTCCGCCGTTATCATGAGAAGCGCATCCGAGCACGCATACTTTCGATCAGTGACTATGTCCTCCGA
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 | 53.00% | 11.60% | 2.62% | 32.78% | NA |
| All Indica | 2759 | 44.90% | 4.30% | 3.99% | 46.72% | NA |
| All Japonica | 1512 | 62.40% | 26.30% | 0.33% | 11.04% | NA |
| Aus | 269 | 92.60% | 0.00% | 0.00% | 7.43% | NA |
| Indica I | 595 | 26.20% | 0.20% | 3.87% | 69.75% | NA |
| Indica II | 465 | 55.50% | 1.50% | 3.66% | 39.35% | NA |
| Indica III | 913 | 51.50% | 9.40% | 5.04% | 34.06% | NA |
| Indica Intermediate | 786 | 45.30% | 3.30% | 3.05% | 48.35% | NA |
| Temperate Japonica | 767 | 93.00% | 0.70% | 0.13% | 6.26% | NA |
| Tropical Japonica | 504 | 8.70% | 74.80% | 0.60% | 15.87% | NA |
| Japonica Intermediate | 241 | 77.20% | 6.20% | 0.41% | 16.18% | NA |
| VI/Aromatic | 96 | 31.20% | 12.50% | 7.29% | 48.96% | NA |
| Intermediate | 90 | 45.60% | 23.30% | 2.22% | 28.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0519671296 | C -> T | LOC_Os05g33490.1 | missense_variant ; p.Arg1938Gln; MODERATE | nonsynonymous_codon ; R1938Q | Average:11.577; most accessible tissue: Minghui63 panicle, score: 20.733 | benign  |
0.765 |
TOLERATED | 0.07 |
| vg0519671296 | C -> DEL | LOC_Os05g33490.1 | N | frameshift_variant | Average:11.577; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0519671296 | 6.40E-07 | 6.40E-07 | mr1300 | 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 |
| vg0519671296 | NA | 3.09E-07 | mr1551 | 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 |
| vg0519671296 | NA | 3.47E-06 | mr1398_2 | 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 |