Search for Variation information by Variation ID:
Detailed information for vg0623262186:
| Variant ID: vg0623262186 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 23262186 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GCGTCTTCCTATTTATCGTCCAGAAGACCACCGATTCGTGTGGTCTTGGACGGGCCGTCGCCCAGGGCAACCTCCTTGACCGGGACCTCGTCGCACGTGA[C/T]
CATCCGCTGCCTCGGGGCGGCGGGGACGGAGGTGCCGAGCCTTTCGTCGCCACCCGTGGGCTTGGACGCCGCGGCGAGGTGGTACGCGCGCTGCTCCATA
Reverse complement sequence
TATGGAGCAGCGCGCGTACCACCTCGCCGCGGCGTCCAAGCCCACGGGTGGCGACGAAAGGCTCGGCACCTCCGTCCCCGCCGCCCCGAGGCAGCGGATG[G/A]
TCACGTGCGACGAGGTCCCGGTCAAGGAGGTTGCCCTGGGCGACGGCCCGTCCAAGACCACACGAATCGGTGGTCTTCTGGACGATAAATAGGAAGACGC
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 | 63.50% | 2.10% | 6.37% | 28.08% | NA |
| All Indica | 2759 | 69.70% | 2.50% | 7.47% | 20.30% | NA |
| All Japonica | 1512 | 49.60% | 1.60% | 4.89% | 43.92% | NA |
| Aus | 269 | 88.10% | 0.40% | 1.86% | 9.67% | NA |
| Indica I | 595 | 70.60% | 1.00% | 4.87% | 23.53% | NA |
| Indica II | 465 | 58.90% | 3.00% | 8.82% | 29.25% | NA |
| Indica III | 913 | 78.50% | 2.50% | 8.65% | 10.30% | NA |
| Indica Intermediate | 786 | 65.10% | 3.40% | 7.25% | 24.17% | NA |
| Temperate Japonica | 767 | 51.80% | 0.10% | 1.96% | 46.15% | NA |
| Tropical Japonica | 504 | 51.40% | 3.80% | 9.33% | 35.52% | NA |
| Japonica Intermediate | 241 | 39.00% | 1.70% | 4.98% | 54.36% | NA |
| VI/Aromatic | 96 | 30.20% | 0.00% | 10.42% | 59.38% | NA |
| Intermediate | 90 | 67.80% | 3.30% | 6.67% | 22.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0623262186 | C -> T | LOC_Os06g39180.1 | missense_variant ; p.Val724Ile; MODERATE | nonsynonymous_codon ; V724I | Average:14.52; most accessible tissue: Zhenshan97 root, score: 23.888 | benign  |
0.127 |
TOLERATED | 0.88 |
| vg0623262186 | C -> DEL | LOC_Os06g39180.1 | N | frameshift_variant | Average:14.52; most accessible tissue: Zhenshan97 root, score: 23.888 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0623262186 | 6.59E-06 | NA | mr1458_2 | 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 |
| vg0623262186 | 3.73E-06 | NA | mr1458_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 |