21 variations found. LOC_Os10g14290 (expressed protein), ranging from 7,738,294 bp to 7,740,244 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1007738360 (J) | chr10 | 7738360 | C | Unkown | 87.20% | 10.37% | C -> A | NA |
LOC_Os10g14290.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os10g14260.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g14280.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g14270.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os10g14295.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 6.018; most accessible tissue: Minghui63 young leaf, score: 12.713 |
| vg1007738361 (J) | chr10 | 7738361 | G | A | 87.30% | 10.30% | G -> A | NA |
LOC_Os10g14290.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g14290.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.018; most accessible tissue: Minghui63 young leaf, score: 12.713 |
| vg1007738365 (J) | chr10 | 7738365 | T | A | 87.60% | 10.30% | T -> A | NA |
LOC_Os10g14290.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g14290.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.018; most accessible tissue: Minghui63 young leaf, score: 12.713 |
| vg1007738391 (J) | chr10 | 7738391 | G | C | 29.90% | 29.09% | G -> C,T | NA |
LOC_Os10g14290.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g14290.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os10g14290.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.018; most accessible tissue: Minghui63 young leaf, score: 12.713 |
| vg1007738693 (J) | chr10 | 7738693 | C | T | 84.30% | 12.12% | C -> T | NA |
LOC_Os10g14290.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g14290.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.415; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1007738707 (J) | chr10 | 7738707 | G | A | 83.50% | 10.88% | G -> A | NA |
LOC_Os10g14290.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g14290.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.415; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1007738723 (J) | chr10 | 7738723 | G | A | 84.40% | 10.52% | G -> A | NA |
LOC_Os10g14290.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os10g14290.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.415; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1007738748 (J) | chr10 | 7738748 | C | G | 69.10% | 13.58% | C -> G | NA |
LOC_Os10g14290.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g14290.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os10g14290.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.415; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1007738749 (J) | chr10 | 7738749 | T | G | 69.30% | 13.46% | T -> G,C | NA |
LOC_Os10g14290.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g14290.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os10g14290.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.415; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1007738762 (J) | chr10 | 7738762 | C | T | 78.70% | 14.88% | C -> T | NA |
LOC_Os10g14290.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g14290.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.415; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1007738770 (J) | chr10 | 7738770 | G | C | 71.20% | 18.03% | G -> C | NA |
LOC_Os10g14290.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g14290.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.415; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1007738795 (J) | chr10 | 7738795 | G | A | 29.50% | 29.20% | G -> A | NA |
LOC_Os10g14290.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g14290.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.415; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1007739438 (J) | chr10 | 7739438 | C | T | 93.50% | 5.08% | C -> T | NA |
LOC_Os10g14280.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g14270.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g14295.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g14290.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.372; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1007739450 (J) | chr10 | 7739450 | C | T | 93.60% | 6.09% | C -> T | NA |
LOC_Os10g14280.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g14270.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g14295.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g14290.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.372; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1007739452 (J) | chr10 | 7739452 | G | A | 93.70% | 6.09% | G -> A | NA |
LOC_Os10g14280.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g14270.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g14295.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g14290.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.372; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1007739482 (J) | chr10 | 7739482 | T | G | 93.60% | 6.07% | T -> G | NA |
LOC_Os10g14280.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g14270.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g14295.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g14290.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.372; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1007739811 (J) | chr10 | 7739811 | A | G | 93.40% | 6.24% | A -> G | NA |
LOC_Os10g14290.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g14290.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.203; most accessible tissue: Callus, score: 12.568 |
| vg1007739818 (J) | chr10 | 7739818 | A | C | 92.70% | 6.09% | A -> C | NA |
LOC_Os10g14290.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g14290.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.203; most accessible tissue: Callus, score: 12.568 |
| vg1007739850 (J) | chr10 | 7739850 | C | T | 92.90% | 6.07% | C -> T | NA |
LOC_Os10g14290.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os10g14290.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.203; most accessible tissue: Callus, score: 12.562 |
| vg1007739863 (J) | chr10 | 7739863 | C | T | 93.70% | 6.07% | C -> T | NA |
LOC_Os10g14290.1 Alt: T| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os10g14280.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g14270.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g14295.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 5.203; most accessible tissue: Callus, score: 12.562 |
| vg1007739888 (J) | chr10 | 7739888 | G | A | 93.40% | 6.09% | G -> A,T | NA |
LOC_Os10g14280.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g14270.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g14295.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g14290.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g14280.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g14270.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g14295.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g14290.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 5.203; most accessible tissue: Callus, score: 12.562 |