15 variations found. LOC_Os01g63040 (expressed protein), ranging from 36,517,339 bp to 36,521,886 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0136517574 (J) | chr01 | 36517574 | T | C | 36.90% | 55.50% | T -> C | NA |
LOC_Os01g63040.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g63040.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 4.359; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0136517682 (J) | chr01 | 36517682 | A | T | 39.30% | 9.75% | A -> T | NA |
LOC_Os01g63030.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g63040.1 Alt: T| 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 |
| vg0136518367 (J) | chr01 | 36518367 | G | A | 36.90% | 54.57% | G -> A | NA |
LOC_Os01g63040.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os01g63040.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.669; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0136518492 (J) | chr01 | 36518492 | A | G | 35.20% | 58.95% | A -> G | NA |
LOC_Os01g63040.1 Alt: G| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os01g63030.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.903; most accessible tissue: Callus, score: 9.262 |
| vg0136519139 (J) | chr01 | 36519139 | C | T | 36.50% | 56.75% | C -> T | NA |
LOC_Os01g63040.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g63040.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.671; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0136519161 (J) | chr01 | 36519161 | G | A | 36.00% | 57.28% | G -> A | NA |
LOC_Os01g63040.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g63040.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.671; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0136519513 (J) | chr01 | 36519513 | A | G | 9.10% | 67.99% | A -> G | NA |
LOC_Os01g63040.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g63040.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.165; most accessible tissue: Zhenshan97 root, score: 12.891 |
| vg0136519596 (J) | chr01 | 36519596 | G | A | 29.80% | 59.48% | G -> A | NA |
LOC_Os01g63040.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os01g63040.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.947; most accessible tissue: Zhenshan97 root, score: 12.891 |
| vg0136520357 (J) | chr01 | 36520357 | G | A | 34.20% | 60.33% | G -> A | NA |
LOC_Os01g63040.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os01g63040.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0136520805 (J) | chr01 | 36520805 | A | T | 48.60% | 34.79% | A -> T | NA |
LOC_Os01g63030.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g63040.1 Alt: T| 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 |
| vg0136520925 (J) | chr01 | 36520925 | C | T | 35.40% | 60.52% | C -> T | NA |
LOC_Os01g63030.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g63040.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.790; most accessible tissue: Callus, score: 8.026 |
| vg0136521260 (J) | chr01 | 36521260 | A | T | 34.30% | 58.93% | A -> T | NA |
LOC_Os01g63030.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g63040.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 5.515; most accessible tissue: Callus, score: 15.990 |
| vg0136521451 (J) | chr01 | 36521451 | G | A | 44.80% | 47.00% | G -> A | NA |
LOC_Os01g63030.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g63040.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 5.145; most accessible tissue: Callus, score: 11.929 |
| vg0136521761 (J) | chr01 | 36521761 | C | T | 38.20% | 50.00% | C -> T | NA |
LOC_Os01g63040.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g63040.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.802; most accessible tissue: Callus, score: 8.148 |
| vg0136521829 (J) | chr01 | 36521829 | C | T | 46.30% | 46.40% | C -> T | NA |
LOC_Os01g63040.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g63040.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.799; most accessible tissue: Callus, score: 8.115 |