15 variations found. LOC_Os03g60010 (transposon protein; putative; CACTA; En%2FSpm sub-class; expressed), ranging from 34,132,431 bp to 34,135,933 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0334132441 (J) | chr03 | 34132441 | C | T | 47.30% | 47.69% | C -> T | NA |
LOC_Os03g60010.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os03g60010.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 12.835; most accessible tissue: Zhenshan97 root, score: 20.427 |
| vg0334132493 (J) | chr03 | 34132493 | A | ATTTT | 48.10% | 44.46% | A -> ATTTT | NA |
LOC_Os03g60010.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g60010.1 Alt: ATTTT| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 12.835; most accessible tissue: Zhenshan97 root, score: 20.427 |
| vg0334132528 (J) | chr03 | 34132528 | G | A | 46.30% | 51.31% | G -> A | NA |
LOC_Os03g60010.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g60010.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 12.835; most accessible tissue: Zhenshan97 root, score: 20.427 |
| vg0334132972 (J) | chr03 | 34132972 | A | G | 7.10% | 73.44% | G -> A | NA |
LOC_Os03g60010.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g60010.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.769; most accessible tissue: Minghui63 young leaf, score: 9.976 |
| vg0334133366 (J) | chr03 | 34133366 | T | C | 21.80% | 68.66% | C -> T | NA |
LOC_Os03g60010.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g60010.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.720; most accessible tissue: Minghui63 flower, score: 9.270 |
| vg0334133715 (J) | chr03 | 34133715 | A | G | 19.00% | 65.74% | G -> A | NA |
LOC_Os03g60010.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g60010.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0334133761 (J) | chr03 | 34133761 | A | G | 17.10% | 67.44% | G -> A | NA |
LOC_Os03g60010.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g60010.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0334133944 (J) | chr03 | 34133944 | C | T | 2.70% | 86.88% | C -> T | NA |
LOC_Os03g60010.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g60010.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.391; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0334134011 (J) | chr03 | 34134011 | G | A | 2.00% | 75.03% | G -> A | NA |
LOC_Os03g60010.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os03g60010.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.173; most accessible tissue: Minghui63 flower, score: 7.958 |
| vg0334134018 (J) | chr03 | 34134018 | G | A | 0.60% | 81.15% | G -> A | NA |
LOC_Os03g60010.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g60010.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.173; most accessible tissue: Minghui63 flower, score: 7.958 |
| vg0334134348 (J) | chr03 | 34134348 | G | T | 6.70% | 71.77% | G -> T | NA |
LOC_Os03g60010.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g60010.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 21.921; most accessible tissue: Zhenshan97 root, score: 34.536 |
| vg0334134764 (J) | chr03 | 34134764 | G | A | 2.20% | 89.76% | G -> A | NA |
LOC_Os03g60010.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g60010.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.152; most accessible tissue: Zhenshan97 root, score: 12.891 |
| vg0334134781 (J) | chr03 | 34134781 | G | A | 1.50% | 82.37% | G -> A | NA |
LOC_Os03g60010.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g60010.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.934; most accessible tissue: Zhenshan97 root, score: 12.891 |
| vg0334134799 (J) | chr03 | 34134799 | G | T | 1.00% | 93.06% | G -> T | NA |
LOC_Os03g60010.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os03g60010.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.718; most accessible tissue: Zhenshan97 root, score: 10.511 |
| vg0334135606 (J) | chr03 | 34135606 | G | A | 43.80% | 46.45% | G -> A | NA |
LOC_Os03g60010.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g60010.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |