10 variations found. LOC_Os12g06080 (expressed protein), ranging from 2,836,020 bp to 2,836,995 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1202836111 (J) | chr12 | 2836111 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os12g06080.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os12g06070.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 72.266; most accessible tissue: Minghui63 panicle, score: 85.556 |
| vg1202836137 (J) | chr12 | 2836137 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os12g06080.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 72.426; most accessible tissue: Minghui63 panicle, score: 84.552 |
| vg1202836219 (J) | chr12 | 2836219 | T | G | 91.30% | 0.00% | T -> G |
LOC_Os12g06080.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 75.255; most accessible tissue: Minghui63 panicle, score: 84.005 |
|
| vg1202836274 (J) | chr12 | 2836274 | A | G | 99.80% | 0.00% | A -> G | NA |
LOC_Os12g06070.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
LOC_Os12g06080.1 Alt: G| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 77.228; most accessible tissue: Zhenshan97 flower, score: 85.807 |
| vg1202836288 (J) | chr12 | 2836288 | T | C | 94.80% | 0.00% | T -> C | NA |
LOC_Os12g06070.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g06080.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 77.118; most accessible tissue: Zhenshan97 flower, score: 86.268 |
| vg1202836464 (J) | chr12 | 2836464 | C | A | 99.80% | 0.00% | C -> A | NA |
LOC_Os12g06080.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 76.372; most accessible tissue: Zhenshan97 flower, score: 87.550 |
| vg1202836573 (J) | chr12 | 2836573 | G | A | 98.80% | 0.00% | G -> A | NA |
LOC_Os12g06080.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 80.863; most accessible tissue: Zhenshan97 panicle, score: 90.061 |
| vg1202836786 (J) | chr12 | 2836786 | A | G | 89.40% | 0.00% | A -> G |
LOC_Os12g06080.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 83.803; most accessible tissue: Zhenshan97 panicle, score: 92.270 |
|
| vg1202836800 (J) | chr12 | 2836800 | C | T | 92.90% | 0.00% | C -> T | NA |
LOC_Os12g06080.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 83.882; most accessible tissue: Zhenshan97 panicle, score: 92.270 |
| STR1202836794 (J) | chr12 | 2836794 | CGCCGCC GCCGA | CGCCGCT GCCGA | 93.20% | 0.00% | CGCCGCCGCC GA -> CGCCGCTGCC GA | NA |
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