20 variations found. LOC_Os07g32740 (transposon protein; putative; CACTA; En%2FSpm sub-class; expressed), ranging from 19,561,043 bp to 19,563,106 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0719561182 (J) | chr07 | 19561182 | G | A | 19.70% | 60.18% | G -> A | NA |
LOC_Os07g32740.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g32740.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 4.449; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0719561597 (J) | chr07 | 19561597 | T | G | 21.50% | 53.60% | T -> G | NA |
LOC_Os07g32740.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g32740.1 Alt: G/stop_gained(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0719561623 (J) | chr07 | 19561623 | C | A | 5.40% | 51.69% | C -> A | NA |
LOC_Os07g32740.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g32740.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0719561643 (J) | chr07 | 19561643 | G | C | 2.50% | 62.95% | C -> G | NA |
LOC_Os07g32740.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g32740.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0719561938 (J) | chr07 | 19561938 | G | A | 22.20% | 28.37% | G -> A | NA |
LOC_Os07g32740.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g32740.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 5.421; most accessible tissue: Callus, score: 10.667 |
| vg0719561972 (J) | chr07 | 19561972 | A | C | 22.20% | 50.99% | A -> C | NA |
LOC_Os07g32740.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g32740.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 5.421; most accessible tissue: Callus, score: 10.667 |
| vg0719562406 (J) | chr07 | 19562406 | A | G | 2.20% | 55.95% | A -> G | NA |
LOC_Os07g32740.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g32740.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 6.027; most accessible tissue: Zhenshan97 root, score: 12.891 |
| vg0719562414 (J) | chr07 | 19562414 | G | A | 0.60% | 64.81% | G -> A | NA |
LOC_Os07g32740.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g32740.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 6.027; most accessible tissue: Zhenshan97 root, score: 12.891 |
| vg0719562525 (J) | chr07 | 19562525 | C | T | 34.10% | 41.03% | C -> T | NA |
LOC_Os07g32740.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g32740.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 6.027; most accessible tissue: Zhenshan97 root, score: 12.891 |
| vg0719562676 (J) | chr07 | 19562676 | C | A | 19.80% | 56.50% | C -> A | NA |
LOC_Os07g32740.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g32740.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 4.947; most accessible tissue: Zhenshan97 root, score: 12.891 |
| vg0719562781 (J) | chr07 | 19562781 | G | A | 22.40% | 53.81% | G -> A | NA |
LOC_Os07g32740.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g32740.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 4.730; most accessible tissue: Zhenshan97 root, score: 10.511 |
| vg0719562787 (J) | chr07 | 19562787 | A | G | 22.40% | 54.25% | A -> G | NA |
LOC_Os07g32740.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g32740.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 4.730; most accessible tissue: Zhenshan97 root, score: 10.511 |
| vg0719562788 (J) | chr07 | 19562788 | C | T | 22.60% | 50.70% | C -> T | NA |
LOC_Os07g32740.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g32740.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 4.730; most accessible tissue: Zhenshan97 root, score: 10.511 |
| vg0719562789 (J) | chr07 | 19562789 | G | A | 21.90% | 57.24% | G -> A | NA |
LOC_Os07g32740.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g32740.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 4.730; most accessible tissue: Zhenshan97 root, score: 10.511 |
| vg0719562804 (J) | chr07 | 19562804 | A | G | 20.10% | 56.67% | A -> G | NA |
LOC_Os07g32740.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g32740.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0719562809 (J) | chr07 | 19562809 | G | A | 19.80% | 61.21% | G -> A | NA |
LOC_Os07g32740.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g32740.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0719562880 (J) | chr07 | 19562880 | G | A | 38.80% | 41.77% | G -> A | NA |
LOC_Os07g32740.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g32740.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0719562918 (J) | chr07 | 19562918 | G | A | 21.30% | 42.36% | G -> A | NA |
LOC_Os07g32740.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g32740.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 6.614; most accessible tissue: Minghui63 flower, score: 10.335 |
| vg0719562979 (J) | chr07 | 19562979 | T | C | 13.10% | 56.92% | T -> C | NA |
LOC_Os07g32740.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g32740.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 7.428; most accessible tissue: Zhenshan97 flag leaf, score: 11.736 |
| vg0719563095 (J) | chr07 | 19563095 | G | A | 25.10% | 39.76% | G -> A | NA |
LOC_Os07g32740.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g32740.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 8.219; most accessible tissue: Zhenshan97 root, score: 12.891 |