10 variations found. LOC_Os09g17420 (retrotransposon protein; putative; unclassified), ranging from 10,657,279 bp to 10,657,870 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0910657292 (J) | chr09 | 10657292 | C | T | 52.70% | 35.15% | C -> T | NA |
LOC_Os09g17420.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g17420.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 8.446; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg0910657380 (J) | chr09 | 10657380 | T | C | 56.00% | 33.37% | T -> C | NA |
LOC_Os09g17420.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g17420.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 7.605; most accessible tissue: Minghui63 root, score: 13.235 |
| vg0910657408 (J) | chr09 | 10657408 | T | C | 56.30% | 33.54% | T -> C | NA |
LOC_Os09g17420.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g17420.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 7.529; most accessible tissue: Minghui63 root, score: 13.235 |
| vg0910657418 (J) | chr09 | 10657418 | G | A | 55.30% | 33.50% | G -> A | NA |
LOC_Os09g17420.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g17420.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 7.299; most accessible tissue: Zhenshan97 flower, score: 11.396 |
| vg0910657428 (J) | chr09 | 10657428 | G | T | 27.30% | 32.54% | G -> T | NA |
LOC_Os09g17420.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g17420.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 8.619; most accessible tissue: Callus, score: 24.426 |
| vg0910657564 (J) | chr09 | 10657564 | A | C | 38.10% | 47.67% | A -> C | NA |
LOC_Os09g17420.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g17420.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 10.434; most accessible tissue: Callus, score: 24.426 |
| vg0910657665 (J) | chr09 | 10657665 | T | C | 38.00% | 47.86% | T -> C | NA |
LOC_Os09g17420.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g17420.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 10.919; most accessible tissue: Callus, score: 20.752 |
| vg0910657672 (J) | chr09 | 10657672 | T | A | 38.00% | 48.14% | T -> A | NA |
LOC_Os09g17420.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g17420.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 10.919; most accessible tissue: Callus, score: 20.752 |
| vg0910657733 (J) | chr09 | 10657733 | C | T | 54.60% | 33.71% | C -> T | NA |
LOC_Os09g17420.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g17420.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 11.560; most accessible tissue: Callus, score: 28.743 |
| vg0910657775 (J) | chr09 | 10657775 | G | A | 33.90% | 35.38% | G -> A | NA |
LOC_Os09g17420.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g17420.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 11.450; most accessible tissue: Callus, score: 28.743 |