13 variations found. LOC_Os08g25330 (retrotransposon protein; putative; Ty3-gypsy subclass), ranging from 15,407,810 bp to 15,412,385 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 |
---|---|---|---|---|---|---|---|---|---|
vg0815409372 (J) | chr08 | 15409372 | C | G | 19.80% | 41.96% | C -> G | NA |
LOC_Os08g25330.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os08g25330.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.719; most accessible tissue: Minghui63 panicle, score: 7.125 |
vg0815410001 (J) | chr08 | 15410001 | T | C | 20.70% | 67.01% | T -> C | NA |
LOC_Os08g25330.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g25330.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.486; most accessible tissue: Minghui63 panicle, score: 7.125 |
vg0815410038 (J) | chr08 | 15410038 | A | C | 16.80% | 71.96% | A -> C | NA |
LOC_Os08g25330.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os08g25330.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.486; most accessible tissue: Minghui63 panicle, score: 7.125 |
vg0815410058 (J) | chr08 | 15410058 | G | A | 20.50% | 66.55% | G -> A | NA |
LOC_Os08g25330.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g25330.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.486; most accessible tissue: Minghui63 panicle, score: 7.125 |
vg0815410076 (J) | chr08 | 15410076 | A | G | 20.50% | 68.37% | A -> G | NA |
LOC_Os08g25330.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g25330.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.467; most accessible tissue: Minghui63 panicle, score: 7.125 |
vg0815410091 (J) | chr08 | 15410091 | T | C | 19.90% | 68.81% | T -> C | NA |
LOC_Os08g25330.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g25330.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.467; most accessible tissue: Minghui63 panicle, score: 7.125 |
vg0815410433 (J) | chr08 | 15410433 | A | G | 20.60% | 67.65% | A -> G | NA |
LOC_Os08g25330.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g25330.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.196; most accessible tissue: Callus, score: 12.491 |
vg0815410455 (J) | chr08 | 15410455 | C | T | 20.20% | 68.41% | C -> T | NA |
LOC_Os08g25330.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os08g25330.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.196; most accessible tissue: Callus, score: 12.491 |
vg0815411375 (J) | chr08 | 15411375 | A | C | 30.40% | 41.94% | A -> C | NA |
LOC_Os08g25330.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g25330.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
vg0815411661 (J) | chr08 | 15411661 | CTAGAGA TCAACTG GT | C | 19.40% | 69.66% | CTAGAGATCA ACTGGT -> C | NA |
LOC_Os08g25330.1 Alt: C| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os08g25330.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.366; most accessible tissue: Minghui63 panicle, score: 7.125 |
vg0815411672 (J) | chr08 | 15411672 | C | T | 18.50% | 73.72% | C -> T | NA |
LOC_Os08g25330.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g25330.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.366; most accessible tissue: Minghui63 panicle, score: 7.125 |
vg0815412247 (J) | chr08 | 15412247 | C | T | 20.10% | 66.10% | C -> T | NA |
LOC_Os08g25330.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os08g25330.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 10.667; most accessible tissue: Zhenshan97 root, score: 20.427 |
vg0815412275 (J) | chr08 | 15412275 | G | A | 26.80% | 65.59% | G -> A | NA |
LOC_Os08g25330.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g25330.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 11.012; most accessible tissue: Zhenshan97 root, score: 20.427 |