17 variations found. LOC_Os06g21050 (retrotransposon protein; putative; Ty3-gypsy subclass; expressed), ranging from 12,160,155 bp to 12,164,056 bp (including 0 kb upstream and 0 kb downstream of the gene).
Color | Explain | Details |
---|---|---|
red | High impact variants defined by snpEff | 'STOP_LOST', 'START_LOST', 'STOP_GAINED', 'FRAME_SHIFT' et. al., the details can be found at http://snpef f.sourceforge.net/SnpEff_manual.html#eff. |
purple | 'Damaging' or 'probably damaging' non-synonymous SNPs defined by PolyPhen-2 | This is a qualitative result of nonsynonymous SNP annotation, where 'damaging' or 'probably damaging' means that the variant is more likely to affect protein function. Details can be found here. |
Var ID | Chrom | Position | Primary Allele | Secondary Allele | Primary Allele Frequency | DEL Frequency | Var | GWAS Results | Effect |
---|---|---|---|---|---|---|---|---|---|
vg0612160189 (J) | chr06 | 12160189 | C | T | 83.30% | 11.21% | C -> T | NA |
LOC_Os06g21050.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g21050.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.878; most accessible tissue: Callus, score: 8.991 |
vg0612160192 (J) | chr06 | 12160192 | T | C | 83.40% | 11.26% | T -> C | NA |
LOC_Os06g21050.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g21050.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.878; most accessible tissue: Callus, score: 8.991 |
vg0612160194 (J) | chr06 | 12160194 | G | A | 83.20% | 11.19% | G -> A | NA |
LOC_Os06g21050.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g21050.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.878; most accessible tissue: Callus, score: 8.991 |
vg0612160204 (J) | chr06 | 12160204 | C | T | 83.30% | 11.51% | C -> T | NA |
LOC_Os06g21050.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g21050.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.878; most accessible tissue: Callus, score: 8.991 |
vg0612160207 (J) | chr06 | 12160207 | A | G | 38.80% | 1.27% | A -> G | NA |
LOC_Os06g21050.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g21050.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.878; most accessible tissue: Callus, score: 8.991 |
vg0612160212 (J) | chr06 | 12160212 | C | T | 82.40% | 11.45% | C -> T,A | NA |
LOC_Os06g21050.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g21050.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os06g21050.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.878; most accessible tissue: Callus, score: 8.991 |
vg0612160213 (J) | chr06 | 12160213 | C | T | 83.50% | 11.24% | C -> T | NA |
LOC_Os06g21050.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g21050.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.878; most accessible tissue: Callus, score: 8.991 |
vg0612160216 (J) | chr06 | 12160216 | A | C | 81.00% | 11.45% | A -> C | NA |
LOC_Os06g21050.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g21050.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.878; most accessible tissue: Callus, score: 8.991 |
vg0612160219 (J) | chr06 | 12160219 | T | C | 82.10% | 11.11% | T -> C | NA |
LOC_Os06g21050.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g21050.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.878; most accessible tissue: Callus, score: 8.991 |
vg0612160225 (J) | chr06 | 12160225 | C | T | 83.90% | 10.81% | C -> T | NA |
LOC_Os06g21050.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g21050.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.878; most accessible tissue: Callus, score: 8.991 |
vg0612160226 (J) | chr06 | 12160226 | G | A | 84.00% | 10.58% | G -> A | NA |
LOC_Os06g21050.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os06g21050.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.878; most accessible tissue: Callus, score: 8.991 |
vg0612160228 (J) | chr06 | 12160228 | T | C | 84.20% | 10.47% | T -> C | NA |
LOC_Os06g21050.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g21050.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.878; most accessible tissue: Callus, score: 8.991 |
vg0612160237 (J) | chr06 | 12160237 | C | T | 80.40% | 14.60% | C -> T | NA |
LOC_Os06g21050.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g21050.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.878; most accessible tissue: Callus, score: 8.991 |
vg0612160243 (J) | chr06 | 12160243 | C | A | 45.80% | 30.70% | C -> T,A | NA |
LOC_Os06g21050.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g21050.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os06g21050.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.878; most accessible tissue: Callus, score: 8.991 |
vg0612160252 (J) | chr06 | 12160252 | G | A | 32.50% | 46.11% | G -> A | NA |
LOC_Os06g21050.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g21050.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.878; most accessible tissue: Callus, score: 8.991 |
vg0612160258 (J) | chr06 | 12160258 | T | C | 38.00% | 37.24% | T -> C | NA |
LOC_Os06g21050.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g21050.1 Alt: C| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os06g21050.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.878; most accessible tissue: Callus, score: 8.991 |
vg0612160260 (J) | chr06 | 12160260 | G | A | 37.60% | 38.68% | G -> A | NA |
LOC_Os06g21050.1 Alt: A| stop_gained HIGH(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g21050.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.878; most accessible tissue: Callus, score: 8.991 |