Search for Variation information by Variation ID:
Detailed information for vg0622756910:
| Variant ID: vg0622756910 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 22756910 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 263. )
Flanking Sequence (100 bp) in Reference Genome:
TAGTCGGCAGCAACTGAAACTACAACAACTCAAGAGCCCCCGACTGGAAACCAGTCGGATGTAGGTCCAGATCAAGAAACTCCCGAAGTTGAAGCGCAGA[C/T]
GACAACTTCTCGAGGACCAGAGGCTGGTAACGACTCGATGATTGGGTCTCCGAATAAAGAACAAGGATCACCTTACGTTCAGCTAGGAACATCCTCAGGT
Reverse complement sequence
ACCTGAGGATGTTCCTAGCTGAACGTAAGGTGATCCTTGTTCTTTATTCGGAGACCCAATCATCGAGTCGTTACCAGCCTCTGGTCCTCGAGAAGTTGTC[G/A]
TCTGCGCTTCAACTTCGGGAGTTTCTTGATCTGGACCTACATCCGACTGGTTTCCAGTCGGGGGCTCTTGAGTTGTTGTAGTTTCAGTTGCTGCCGACTA
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 | 85.20% | 4.30% | 1.31% | 9.20% | NA |
| All Indica | 2759 | 79.70% | 7.20% | 2.10% | 10.98% | NA |
| All Japonica | 1512 | 92.90% | 0.10% | 0.26% | 6.81% | NA |
| Aus | 269 | 92.90% | 0.40% | 0.00% | 6.69% | NA |
| Indica I | 595 | 62.20% | 22.20% | 4.71% | 10.92% | NA |
| Indica II | 465 | 76.30% | 3.40% | 2.37% | 17.85% | NA |
| Indica III | 913 | 90.70% | 1.00% | 0.11% | 8.21% | NA |
| Indica Intermediate | 786 | 82.30% | 5.20% | 2.29% | 10.18% | NA |
| Temperate Japonica | 767 | 93.90% | 0.10% | 0.39% | 5.61% | NA |
| Tropical Japonica | 504 | 97.00% | 0.00% | 0.00% | 2.98% | NA |
| Japonica Intermediate | 241 | 80.90% | 0.00% | 0.41% | 18.67% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 84.40% | 3.30% | 0.00% | 12.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0622756910 | C -> T | LOC_Os06g38410.1 | missense_variant ; p.Thr404Met; MODERATE | nonsynonymous_codon ; T404M | Average:22.377; most accessible tissue: Minghui63 panicle, score: 29.741 | probably damaging  |
2.771 |
DELETERIOUS | 0.01 |
| vg0622756910 | C -> DEL | LOC_Os06g38410.1 | N | frameshift_variant | Average:22.377; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0622756910 | 4.77E-06 | NA | mr1879 | 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 |