Search for Variation information by Variation ID:
Detailed information for vg0621394277:
| Variant ID: vg0621394277 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 21394277 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 386. )
Flanking Sequence (100 bp) in Reference Genome:
GTGCTTCGACTTGCATCCATCATACAACGGCATCTGGCAATCTTCCACCAACTTACTAAACTTCTCATAATCTCTGTCGTTGTCCTCTGCGTCTTCAATG[T/C]
CATGCAACATTGTAGATAGACATTGAGTGTCCAAATCTATGGTCTCTCCACCTAAAGGAGAAGGTACGAACATGCCTTCTCGAGCTGCGGCGGTGTTCTC
Reverse complement sequence
GAGAACACCGCCGCAGCTCGAGAAGGCATGTTCGTACCTTCTCCTTTAGGTGGAGAGACCATAGATTTGGACACTCAATGTCTATCTACAATGTTGCATG[A/G]
CATTGAAGACGCAGAGGACAACGACAGAGATTATGAGAAGTTTAGTAAGTTGGTGGAAGATTGCCAGATGCCGTTGTATGATGGATGCAAGTCGAAGCAC
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 | 0.30% | 0.00% | 4.63% | 95.09% | NA |
| All Indica | 2759 | 0.40% | 0.00% | 2.43% | 97.17% | NA |
| All Japonica | 1512 | 0.10% | 0.10% | 9.72% | 90.15% | NA |
| Aus | 269 | 0.00% | 0.00% | 0.37% | 99.63% | NA |
| Indica I | 595 | 0.00% | 0.00% | 1.68% | 98.32% | NA |
| Indica II | 465 | 1.10% | 0.00% | 2.15% | 96.77% | NA |
| Indica III | 913 | 0.50% | 0.00% | 2.96% | 96.50% | NA |
| Indica Intermediate | 786 | 0.10% | 0.00% | 2.54% | 97.33% | NA |
| Temperate Japonica | 767 | 0.00% | 0.00% | 3.39% | 96.61% | NA |
| Tropical Japonica | 504 | 0.20% | 0.20% | 14.68% | 84.92% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.00% | 19.50% | 80.50% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 1.04% | 98.96% | NA |
| Intermediate | 90 | 0.00% | 0.00% | 3.33% | 96.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0621394277 | T -> C | LOC_Os06g36440.1 | missense_variant ; p.Asp129Gly; MODERATE | nonsynonymous_codon ; D129G | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | possibly damaging  |
1.551 |
DELETERIOUS | 0.00 |
| vg0621394277 | T -> DEL | LOC_Os06g36440.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |