2 variations found. LOC_Os08g36880 (transposon protein; putative; CACTA; En%2FSpm sub-class), ranging from 23,301,886 bp to 23,303,467 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0823302212 (J) | chr08 | 23302212 | GTATATA TATATA | GTATA | 22.90% | 54.25% | GTATATATAT ATA -> GTATATATA, GTATATA,GT ATA,GTA,G | NA |
LOC_Os08g36870.1 Alt: GTATATATA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g36880.1 Alt: GTATATATA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os08g36870.1 Alt: GTATATA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g36880.1 Alt: GTATATA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g36870.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g36880.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g36870.1 Alt: GTA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g36880.1 Alt: GTA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g36870.1 Alt: GTATA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g36880.1 Alt: GTATA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.386; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0823303282 (J) | chr08 | 23303282 | C | T | 29.50% | 55.40% | C -> T | NA |
LOC_Os08g36880.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g36880.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.371; most accessible tissue: Minghui63 panicle, score: 7.125 |