9 variations found. LOC_Os02g54400 (transposon protein; putative; CACTA; En%2FSpm sub-class; expressed), ranging from 33,333,957 bp to 33,337,658 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0233334140 (J) | chr02 | 33334140 | T | C | 35.90% | 63.20% | T -> C | NA |
LOC_Os02g54400.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g54400.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 5.739; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg0233334543 (J) | chr02 | 33334543 | C | A | 35.90% | 63.25% | C -> A | NA |
LOC_Os02g54390.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54400.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 6.222; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg0233335725 (J) | chr02 | 33335725 | C | T | 36.20% | 62.89% | C -> T | NA |
LOC_Os02g54400.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g54400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.532; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0233335734 (J) | chr02 | 33335734 | TG | T | 34.70% | 62.89% | TG -> T | NA |
LOC_Os02g54400.1 Alt: T| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os02g54400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.532; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0233336095 (J) | chr02 | 33336095 | CCTGCTG GAATCGG CCTGCAG TGGTAAG TACCTAA AGGG | C | 36.30% | 62.70% | CCTGCTGGAA TCGGCCTGCA GTGGTAAGTA CCTAAAGGG -> C | NA |
LOC_Os02g54400.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g54400.1 Alt: C| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 7.027; most accessible tissue: Zhenshan97 root, score: 16.934 |
| vg0233336106 (J) | chr02 | 33336106 | C | T | 34.90% | 62.72% | C -> T | NA |
LOC_Os02g54400.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g54400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 7.027; most accessible tissue: Zhenshan97 root, score: 16.934 |
| vg0233336136 (J) | chr02 | 33336136 | C | CT | 36.10% | 62.57% | C -> CT | NA |
LOC_Os02g54400.1 Alt: CT| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os02g54400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 7.027; most accessible tissue: Zhenshan97 root, score: 16.934 |
| vg0233336536 (J) | chr02 | 33336536 | C | T | 35.70% | 57.24% | C -> T | NA |
LOC_Os02g54400.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g54400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.518; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0233336952 (J) | chr02 | 33336952 | A | G | 4.60% | 67.71% | G -> A | NA |
LOC_Os02g54400.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g54400.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 7.985; most accessible tissue: Callus, score: 17.725 |