5 variations found. LOC_Os02g07628 (gamma-thionin family domain containing protein; expressed), ranging from 3,948,761 bp to 3,949,211 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0203948852 (J) | chr02 | 3948852 | C | T | 99.60% | 0.00% | C -> T | NA |
LOC_Os02g07620.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g07624.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g07630.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g07628.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.303; most accessible tissue: Zhenshan97 panicle, score: 86.058 |
| vg0203949091 (J) | chr02 | 3949091 | A | AG | 94.40% | 0.00% | A -> AG | NA |
LOC_Os02g07628.1 Alt: AG| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 81.774; most accessible tissue: Zhenshan97 panicle, score: 89.143 |
| vg0203949121 (J) | chr02 | 3949121 | C | A | 72.90% | 0.15% | C -> A |
LOC_Os02g07628.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os02g07628.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 81.980; most accessible tissue: Zhenshan97 panicle, score: 88.625 |
|
| vg0203949192 (J) | chr02 | 3949192 | TGAC | T | 96.30% | 0.00% | TGAC -> T | NA |
LOC_Os02g07628.1 Alt: T| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 83.110; most accessible tissue: Callus, score: 91.281 |
| STR0203949193 (J) | chr02 | 3949193 | GACGACG AC | GACGAC | 99.20% | 0.00% | GACGACGAC -> GACGAC | NA |
|