9 variations found. LOC_Os02g15470 (transposon protein; putative; CACTA; En%2FSpm sub-class; expressed), ranging from 8,664,543 bp to 8,667,608 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0208664610 (J) | chr02 | 8664610 | C | G | 13.00% | 79.58% | C -> G | NA |
LOC_Os02g15470.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g15470.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.663; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0208664960 (J) | chr02 | 8664960 | C | T | 24.80% | 72.87% | C -> T | NA |
LOC_Os02g15470.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g15470.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.469; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0208664969 (J) | chr02 | 8664969 | C | T | 24.50% | 68.32% | C -> T | NA |
LOC_Os02g15470.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g15470.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.469; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0208664984 (J) | chr02 | 8664984 | G | A | 24.30% | 68.32% | G -> A | NA |
LOC_Os02g15470.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g15470.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.469; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0208665038 (J) | chr02 | 8665038 | C | T | 8.40% | 81.82% | C -> T | NA |
LOC_Os02g15470.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g15470.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.469; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0208665452 (J) | chr02 | 8665452 | G | T | 20.30% | 62.74% | G -> T | NA |
LOC_Os02g15470.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os02g15470.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 14.491; most accessible tissue: Minghui63 root, score: 21.615 |
| vg0208665681 (J) | chr02 | 8665681 | G | A | 19.80% | 77.61% | G -> A | NA |
LOC_Os02g15470.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g15470.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 11.112; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg0208667468 (J) | chr02 | 8667468 | C | T | 5.80% | 85.25% | C -> T | NA |
LOC_Os02g15470.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g15470.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0208667471 (J) | chr02 | 8667471 | C | T | 5.80% | 85.25% | C -> T | NA |
LOC_Os02g15470.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g15470.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |