Search for Variation information by Variation ID:
Detailed information for vg1205975370:
| Variant ID: vg1205975370 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 5975370 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TTCTCAGTTAGCCGATTTAGCTTTTCAGGGGTTGATAGCACCAATCAAAGAAAAGTTTTCGGCTCAAGATTTTGAGAGTTTATCTCATCTTGCACAAAAG[G/T]
TGACTCTACATGAGCAAAGGTTTGCTGAGGCAAAGAAGAACTTCAAGAAAATCAATCATGTATATCCTTACATGTATGATTCTGATGATGAGGATGATGA
Reverse complement sequence
TCATCATCCTCATCATCAGAATCATACATGTAAGGATATACATGATTGATTTTCTTGAAGTTCTTCTTTGCCTCAGCAAACCTTTGCTCATGTAGAGTCA[C/A]
CTTTTGTGCAAGATGAGATAAACTCTCAAAATCTTGAGCCGAAAACTTTTCTTTGATTGGTGCTATCAACCCCTGAAAAGCTAAATCGGCTAACTGAGAA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 61.20% | 2.00% | 4.34% | 32.44% | NA |
| All Indica | 2759 | 57.20% | 3.30% | 5.98% | 33.60% | NA |
| All Japonica | 1512 | 72.00% | 0.00% | 0.40% | 27.65% | NA |
| Aus | 269 | 48.30% | 0.00% | 9.29% | 42.38% | NA |
| Indica I | 595 | 48.60% | 4.00% | 5.04% | 42.35% | NA |
| Indica II | 465 | 53.10% | 1.10% | 5.59% | 40.22% | NA |
| Indica III | 913 | 66.70% | 3.00% | 7.34% | 23.00% | NA |
| Indica Intermediate | 786 | 55.00% | 4.30% | 5.34% | 35.37% | NA |
| Temperate Japonica | 767 | 59.60% | 0.00% | 0.26% | 40.16% | NA |
| Tropical Japonica | 504 | 86.70% | 0.00% | 0.79% | 12.50% | NA |
| Japonica Intermediate | 241 | 80.50% | 0.00% | 0.00% | 19.50% | NA |
| VI/Aromatic | 96 | 45.80% | 1.00% | 3.12% | 50.00% | NA |
| Intermediate | 90 | 61.10% | 3.30% | 6.67% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1205975370 | G -> DEL | LOC_Os12g11080.1 | N | frameshift_variant | Average:8.523; most accessible tissue: Callus, score: 21.242 | N | N | N | N |
| vg1205975370 | G -> T | LOC_Os12g11080.1 | missense_variant ; p.Val180Leu; MODERATE | nonsynonymous_codon ; V180L | Average:8.523; most accessible tissue: Callus, score: 21.242 | benign  |
0.139 |
DELETERIOUS | 0.03 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1205975370 | 4.37E-06 | 4.37E-06 | mr1027 | 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 |