5 variations found. LOC_Os03g12480 (expressed protein), ranging from 6,597,842 bp to 6,600,946 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0306598441 (J) | chr03 | 6598441 | G | A | 32.70% | 48.54% | G -> A | NA |
LOC_Os03g12470.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g12490.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g12480.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.917; most accessible tissue: Callus, score: 9.417 |
| vg0306598450 (J) | chr03 | 6598450 | A | G | 29.70% | 48.79% | A -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os03g12470.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g12490.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g12480.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.917; most accessible tissue: Callus, score: 9.417 |
| vg0306598647 (J) | chr03 | 6598647 | C | T | 53.00% | 43.69% | C -> T | NA |
LOC_Os03g12480.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os03g12480.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.378; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0306599712 (J) | chr03 | 6599712 | C | T | 32.00% | 49.13% | C -> T | NA |
LOC_Os03g12490.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g12480.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.407; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0306600589 (J) | chr03 | 6600589 | G | A | 39.20% | 46.85% | G -> A | NA |
LOC_Os03g12490.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g12480.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |