Search for Variation information by Variation ID:
Detailed information for vg1000734007:
| Variant ID: vg1000734007 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 734007 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGCGGCCTCGTTGAAGGAGGGCGTTGCCCGGGAGGCGTCCGACACGGCCATTGTCATTGCTGCTGCCACGACCAGCGGCAGCAAGGTTCCGAAGAAGGGG[A/T]
GGAAGTTTTCCTCCGTGCTCGGCAACCGCCGGAAGACGCCCACTCCATCGGTAAGCTTTCTAGGTTATTGATTTACGTAGTTGGAGAATGTCGCCCTCAT
Reverse complement sequence
ATGAGGGCGACATTCTCCAACTACGTAAATCAATAACCTAGAAAGCTTACCGATGGAGTGGGCGTCTTCCGGCGGTTGCCGAGCACGGAGGAAAACTTCC[T/A]
CCCCTTCTTCGGAACCTTGCTGCCGCTGGTCGTGGCAGCAGCAATGACAATGGCCGTGTCGGACGCCTCCCGGGCAACGCCCTCCTTCAACGAGGCCGCC
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 85.40% | 4.70% | 1.95% | 7.91% | NA |
| All Indica | 2759 | 76.40% | 7.80% | 3.12% | 12.65% | NA |
| All Japonica | 1512 | 98.20% | 0.10% | 0.26% | 1.39% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 71.40% | 8.90% | 1.85% | 17.82% | NA |
| Indica II | 465 | 63.70% | 17.00% | 3.23% | 16.13% | NA |
| Indica III | 913 | 83.20% | 2.50% | 4.38% | 9.86% | NA |
| Indica Intermediate | 786 | 79.80% | 7.80% | 2.54% | 9.92% | NA |
| Temperate Japonica | 767 | 97.70% | 0.30% | 0.26% | 1.83% | NA |
| Tropical Japonica | 504 | 99.60% | 0.00% | 0.20% | 0.20% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.00% | 0.41% | 2.49% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 88.90% | 4.40% | 2.22% | 4.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1000734007 | A -> T | LOC_Os10g02150.1 | missense_variant ; p.Arg197Trp; MODERATE | nonsynonymous_codon ; R197W | Average:37.787; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 | probably damaging  |
3.422 |
DELETERIOUS | 0.00 |
| vg1000734007 | A -> DEL | LOC_Os10g02150.1 | N | frameshift_variant | Average:37.787; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1000734007 | 2.61E-06 | 5.47E-07 | mr1622_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 |