28 variations found. LOC_Os12g07170 (transposon protein; putative; Pong sub-class; expressed), ranging from 3,523,302 bp to 3,525,424 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1203523310 (J) | chr12 | 3523310 | G | A | 94.50% | 4.63% | G -> A | NA |
LOC_Os12g07170.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g07170.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 9.605; most accessible tissue: Zhenshan97 panicle, score: 20.424 |
| vg1203523394 (J) | chr12 | 3523394 | T | Unkown | 94.50% | 5.14% | T -> C | NA |
LOC_Os12g07170.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os12g07160.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g07160.2 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g07180.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 11.256; most accessible tissue: Zhenshan97 panicle, score: 28.447 |
| vg1203523483 (J) | chr12 | 3523483 | G | A | 98.90% | 0.21% | G -> A | NA |
LOC_Os12g07170.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os12g07160.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g07160.2 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g07180.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 14.808; most accessible tissue: Zhenshan97 panicle, score: 32.308 |
| vg1203523491 (J) | chr12 | 3523491 | G | A | 99.20% | 0.21% | G -> A | NA |
LOC_Os12g07170.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os12g07160.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g07160.2 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g07180.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 15.309; most accessible tissue: Zhenshan97 panicle, score: 32.308 |
| vg1203523516 (J) | chr12 | 3523516 | G | A | 92.40% | 3.83% | G -> A | NA |
LOC_Os12g07170.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g07170.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 15.784; most accessible tissue: Zhenshan97 panicle, score: 32.308 |
| vg1203523526 (J) | chr12 | 3523526 | C | T | 93.30% | 0.32% | C -> T | NA |
LOC_Os12g07170.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g07170.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 15.851; most accessible tissue: Zhenshan97 panicle, score: 32.308 |
| vg1203523533 (J) | chr12 | 3523533 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os12g07170.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os12g07160.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g07160.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g07180.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 15.905; most accessible tissue: Zhenshan97 panicle, score: 32.308 |
| vg1203523726 (J) | chr12 | 3523726 | T | Unkown | 94.90% | 4.89% | T -> G | NA |
LOC_Os12g07170.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os12g07160.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g07160.2 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g07180.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 17.217; most accessible tissue: Zhenshan97 panicle, score: 28.447 |
| vg1203523727 (J) | chr12 | 3523727 | G | Unkown | 94.90% | 4.91% | G -> A | NA |
LOC_Os12g07170.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os12g07160.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g07160.2 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g07180.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 17.035; most accessible tissue: Zhenshan97 panicle, score: 28.447 |
| vg1203523729 (J) | chr12 | 3523729 | G | Unkown | 94.90% | 4.91% | G -> C | NA |
LOC_Os12g07170.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os12g07160.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g07160.2 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g07180.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 16.970; most accessible tissue: Zhenshan97 panicle, score: 28.447 |
| vg1203523765 (J) | chr12 | 3523765 | G | T | 94.60% | 5.06% | G -> T | NA |
LOC_Os12g07170.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g07170.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 16.551; most accessible tissue: Zhenshan97 root, score: 27.411 |
| vg1203523770 (J) | chr12 | 3523770 | G | A | 94.60% | 5.06% | G -> A | NA |
LOC_Os12g07170.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g07170.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 16.359; most accessible tissue: Zhenshan97 root, score: 25.639 |
| vg1203523888 (J) | chr12 | 3523888 | G | C | 98.10% | 0.02% | G -> C | NA |
LOC_Os12g07170.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os12g07170.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 13.508; most accessible tissue: Zhenshan97 root, score: 20.427 |
| vg1203523897 (J) | chr12 | 3523897 | A | G | 90.30% | 0.00% | A -> G | NA |
LOC_Os12g07170.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 13.305; most accessible tissue: Zhenshan97 root, score: 20.427 |
| vg1203523901 (J) | chr12 | 3523901 | A | G | 99.70% | 0.02% | A -> G | NA |
LOC_Os12g07170.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os12g07160.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g07160.2 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g07180.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 13.083; most accessible tissue: Zhenshan97 root, score: 20.427 |
| vg1203523922 (J) | chr12 | 3523922 | G | Unkown | 99.80% | 0.02% | G -> C | NA |
LOC_Os12g07170.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os12g07160.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g07160.2 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g07180.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 12.911; most accessible tissue: Zhenshan97 root, score: 20.427 |
| vg1203523953 (J) | chr12 | 3523953 | G | T | 99.80% | 0.21% | G -> T | NA |
LOC_Os12g07170.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os12g07160.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g07160.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g07180.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 12.637; most accessible tissue: Zhenshan97 root, score: 20.427 |
| vg1203524065 (J) | chr12 | 3524065 | A | Unkown | 94.90% | 4.66% | A -> G | NA |
LOC_Os12g07170.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os12g07160.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g07160.2 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g07180.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 10.857; most accessible tissue: Zhenshan97 flower, score: 16.600 |
| vg1203524081 (J) | chr12 | 3524081 | C | T | 94.20% | 4.87% | C -> T | NA |
LOC_Os12g07170.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g07170.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 11.153; most accessible tissue: Zhenshan97 flower, score: 16.600 |
| vg1203524093 (J) | chr12 | 3524093 | T | Unkown | 94.90% | 4.87% | T -> A | NA |
LOC_Os12g07170.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os12g07160.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g07160.2 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g07180.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 10.932; most accessible tissue: Zhenshan97 flower, score: 16.600 |
| vg1203524107 (J) | chr12 | 3524107 | C | Unkown | 94.80% | 5.01% | C -> T | NA |
LOC_Os12g07170.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os12g07160.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g07160.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g07180.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 10.855; most accessible tissue: Zhenshan97 flower, score: 15.748 |
| vg1203524128 (J) | chr12 | 3524128 | C | Unkown | 94.60% | 5.04% | C -> T | NA |
LOC_Os12g07170.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os12g07160.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g07160.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g07180.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 10.855; most accessible tissue: Zhenshan97 flower, score: 15.748 |
| vg1203524289 (J) | chr12 | 3524289 | A | T | 91.90% | 0.49% | A -> T | NA |
LOC_Os12g07170.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g07170.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 12.494; most accessible tissue: Callus, score: 23.773 |
| vg1203524293 (J) | chr12 | 3524293 | G | T | 84.90% | 3.39% | G -> T,A | NA |
LOC_Os12g07170.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g07170.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os12g07170.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 12.494; most accessible tissue: Callus, score: 23.773 |
| vg1203524362 (J) | chr12 | 3524362 | A | G | 99.20% | 0.00% | A -> G | NA |
LOC_Os12g07170.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os12g07160.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g07160.2 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g07180.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 12.350; most accessible tissue: Callus, score: 23.451 |
| vg1203524706 (J) | chr12 | 3524706 | G | C | 96.80% | 0.21% | G -> C | NA |
LOC_Os12g07160.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g07160.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g07180.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g07170.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.603; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1203524719 (J) | chr12 | 3524719 | G | A | 89.60% | 0.00% | G -> A | NA |
LOC_Os12g07160.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g07160.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g07180.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g07170.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.603; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1203524747 (J) | chr12 | 3524747 | T | G | 92.10% | 0.21% | T -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g07160.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g07160.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g07180.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g07170.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.603; most accessible tissue: Minghui63 panicle, score: 7.125 |