9 variations found. LOC_Os06g34620 (Zinc finger; C3HC4 type domain containing protein; expressed), ranging from 20,131,643 bp to 20,132,168 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0620131662 (J) | chr06 | 20131662 | TCGACGA | T | 90.50% | 6.79% | TCGACGA -> T | NA |
LOC_Os06g34620.1 Alt: T| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os06g34620.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 77.394; most accessible tissue: Zhenshan97 root, score: 93.096 |
| vg0620131707 (J) | chr06 | 20131707 | G | A | 92.00% | 5.56% | G -> A | NA |
LOC_Os06g34620.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g34620.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 78.111; most accessible tissue: Zhenshan97 root, score: 92.627 |
| vg0620131709 (J) | chr06 | 20131709 | G | T | 91.70% | 5.95% | G -> T | NA |
LOC_Os06g34620.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g34620.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 78.171; most accessible tissue: Zhenshan97 root, score: 92.627 |
| vg0620131842 (J) | chr06 | 20131842 | G | A | 66.80% | 8.23% | A -> G | NA |
LOC_Os06g34620.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g34620.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 74.742; most accessible tissue: Zhenshan97 root, score: 87.558 |
| vg0620131889 (J) | chr06 | 20131889 | G | A | 91.80% | 0.02% | G -> A | NA |
LOC_Os06g34620.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g34620.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 74.285; most accessible tissue: Zhenshan97 root, score: 86.991 |
| vg0620131984 (J) | chr06 | 20131984 | C | T | 72.20% | 6.12% | C -> T | NA |
LOC_Os06g34620.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g34620.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 72.322; most accessible tissue: Zhenshan97 panicle, score: 84.824 |
| vg0620132090 (J) | chr06 | 20132090 | A | G | 69.70% | 11.87% | A -> G | NA |
LOC_Os06g34620.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g34620.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 66.359; most accessible tissue: Zhenshan97 panicle, score: 81.752 |
| vg0620132098 (J) | chr06 | 20132098 | A | G | 69.70% | 13.22% | A -> G | NA |
LOC_Os06g34620.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g34620.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 66.117; most accessible tissue: Zhenshan97 panicle, score: 81.135 |
| vg0620132129 (J) | chr06 | 20132129 | A | G | 69.20% | 14.96% | A -> G | NA |
LOC_Os06g34620.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g34620.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 63.394; most accessible tissue: Zhenshan97 root, score: 77.733 |