23 variations found. LOC_Os03g02350 (transposon protein; putative; unclassified; expressed), ranging from 822,249 bp to 828,405 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0300824097 (J) | chr03 | 824097 | T | C | 11.40% | 86.78% | T -> C | NA |
LOC_Os03g02350.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g02350.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0300824115 (J) | chr03 | 824115 | G | A | 13.10% | 86.35% | G -> A | NA |
LOC_Os03g02350.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g02350.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0300824531 (J) | chr03 | 824531 | G | A | 13.10% | 85.84% | G -> A | NA |
LOC_Os03g02350.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g02350.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0300824792 (J) | chr03 | 824792 | G | A | 13.40% | 85.38% | G -> A | NA |
LOC_Os03g02350.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g02350.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0300824931 (J) | chr03 | 824931 | C | T | 13.60% | 84.81% | C -> T | NA |
LOC_Os03g02350.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g02350.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0300824953 (J) | chr03 | 824953 | C | T | 13.30% | 86.35% | C -> T | NA |
LOC_Os03g02350.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os03g02350.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0300825500 (J) | chr03 | 825500 | G | A | 12.10% | 86.48% | G -> A | NA |
LOC_Os03g02350.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g02350.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0300825584 (J) | chr03 | 825584 | G | A | 17.70% | 78.84% | G -> A | NA |
LOC_Os03g02350.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g02350.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0300825597 (J) | chr03 | 825597 | T | C | 17.80% | 78.59% | T -> C | NA |
LOC_Os03g02350.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g02350.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0300825618 (J) | chr03 | 825618 | A | G | 13.30% | 82.37% | A -> G | NA |
LOC_Os03g02350.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g02350.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0300825644 (J) | chr03 | 825644 | G | A | 13.10% | 82.84% | G -> A | NA |
LOC_Os03g02350.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g02350.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0300825646 (J) | chr03 | 825646 | C | T | 19.10% | 78.10% | C -> T | NA |
LOC_Os03g02350.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g02350.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0300825672 (J) | chr03 | 825672 | C | T | 13.10% | 85.84% | C -> T | NA |
LOC_Os03g02350.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g02350.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0300825951 (J) | chr03 | 825951 | A | G | 15.40% | 81.08% | A -> G | NA |
LOC_Os03g02350.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g02350.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0300825980 (J) | chr03 | 825980 | T | C | 15.90% | 80.66% | T -> C | NA |
LOC_Os03g02350.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g02350.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0300825981 (J) | chr03 | 825981 | G | A | 17.70% | 79.14% | G -> A | NA |
LOC_Os03g02350.1 Alt: A| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g02350.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0300825998 (J) | chr03 | 825998 | A | G | 13.10% | 83.14% | A -> G | NA |
LOC_Os03g02350.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g02350.1 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 |
| vg0300826000 (J) | chr03 | 826000 | G | A | 18.10% | 79.03% | G -> A | NA |
LOC_Os03g02350.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g02350.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0300826009 (J) | chr03 | 826009 | G | A | 21.30% | 75.41% | G -> A | NA |
LOC_Os03g02350.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g02350.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0300826013 (J) | chr03 | 826013 | A | T | 14.60% | 82.63% | A -> T | NA |
LOC_Os03g02350.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g02350.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0300826027 (J) | chr03 | 826027 | A | G | 13.30% | 84.15% | A -> G | NA |
LOC_Os03g02350.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g02350.1 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 |
| vg0300826029 (J) | chr03 | 826029 | C | T | 13.10% | 85.23% | C -> T | NA |
LOC_Os03g02350.1 Alt: T| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g02350.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0300827025 (J) | chr03 | 827025 | T | C | 12.00% | 84.17% | T -> C | NA |
LOC_Os03g02350.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g02350.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |