12 variations found. LOC_Os02g11730 (transposon protein; putative; unclassified; expressed), ranging from 6,041,606 bp to 6,047,544 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0206043262 (J) | chr02 | 6043262 | G | A | 33.40% | 61.66% | G -> A | NA |
LOC_Os02g11730.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g11730.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.476; most accessible tissue: Callus, score: 15.485 |
| vg0206043288 (J) | chr02 | 6043288 | C | T | 33.70% | 60.60% | C -> T | NA |
LOC_Os02g11730.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g11730.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.476; most accessible tissue: Callus, score: 15.485 |
| vg0206043347 (J) | chr02 | 6043347 | C | T | 32.40% | 59.14% | C -> T | NA |
LOC_Os02g11730.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os02g11730.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.066; most accessible tissue: Zhenshan97 root, score: 12.891 |
| vg0206044177 (J) | chr02 | 6044177 | T | A | 31.90% | 63.31% | T -> A | NA |
LOC_Os02g11730.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g11730.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0206044763 (J) | chr02 | 6044763 | C | T | 35.90% | 38.34% | C -> T | NA |
LOC_Os02g11730.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os02g11730.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 16.669; most accessible tissue: Minghui63 panicle, score: 46.754 |
| vg0206045347 (J) | chr02 | 6045347 | G | A | 33.30% | 61.32% | G -> A | NA |
LOC_Os02g11730.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 5.210; most accessible tissue: Callus, score: 9.670 |
| vg0206046813 (J) | chr02 | 6046813 | G | A | 33.30% | 59.67% | G -> A | NA |
LOC_Os02g11730.1 Alt: A| missense_variant&splice_region_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os02g11730.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 11.219; most accessible tissue: Callus, score: 26.200 |
| vg0206047281 (J) | chr02 | 6047281 | G | A | 32.10% | 63.80% | G -> A | NA |
LOC_Os02g11730.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g11730.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.551; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0206047298 (J) | chr02 | 6047298 | C | T | 33.10% | 65.59% | C -> T | NA |
LOC_Os02g11730.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g11730.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.551; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0206047310 (J) | chr02 | 6047310 | T | G | 33.30% | 63.58% | T -> G | NA |
LOC_Os02g11730.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g11730.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.551; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0206047353 (J) | chr02 | 6047353 | C | T | 33.80% | 57.45% | C -> T | NA |
LOC_Os02g11730.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os02g11730.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.423; most accessible tissue: Minghui63 flower, score: 7.958 |
| vg0206047442 (J) | chr02 | 6047442 | A | T | 37.70% | 30.60% | A -> T | NA |
LOC_Os02g11730.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g11730.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.913; most accessible tissue: Minghui63 root, score: 13.235 |