13 variations found. LOC_Os11g24860 (transposon protein; putative; CACTA; En%2FSpm sub-class; expressed), ranging from 14,171,369 bp to 14,174,675 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1114171761 (J) | chr11 | 14171761 | G | A | 34.70% | 63.14% | G -> A | NA |
LOC_Os11g24860.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g24860.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.406; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1114173044 (J) | chr11 | 14173044 | C | T | 3.00% | 84.74% | C -> T | NA |
LOC_Os11g24860.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g24860.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1114173396 (J) | chr11 | 14173396 | C | A | 11.20% | 63.39% | C -> A | NA |
LOC_Os11g24860.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os11g24860.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 7.227; most accessible tissue: Zhenshan97 root, score: 12.891 |
| vg1114173405 (J) | chr11 | 14173405 | T | C | 12.20% | 71.67% | T -> C | NA |
LOC_Os11g24860.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g24860.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 7.227; most accessible tissue: Zhenshan97 root, score: 12.891 |
| vg1114173460 (J) | chr11 | 14173460 | C | A | 8.00% | 85.15% | C -> A | NA |
LOC_Os11g24860.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g24860.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 7.227; most accessible tissue: Zhenshan97 root, score: 12.891 |
| vg1114173466 (J) | chr11 | 14173466 | C | T | 6.70% | 86.23% | C -> T | NA |
LOC_Os11g24860.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g24860.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 7.227; most accessible tissue: Zhenshan97 root, score: 12.891 |
| vg1114173475 (J) | chr11 | 14173475 | G | A | 3.20% | 90.92% | G -> A | NA |
LOC_Os11g24860.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g24860.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 7.227; most accessible tissue: Zhenshan97 root, score: 12.891 |
| vg1114173769 (J) | chr11 | 14173769 | C | T | 35.20% | 59.84% | C -> T | NA |
LOC_Os11g24860.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g24860.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1114173832 (J) | chr11 | 14173832 | A | G | 35.30% | 60.39% | A -> G | NA |
LOC_Os11g24860.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g24860.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1114174000 (J) | chr11 | 14174000 | C | T | 34.70% | 61.51% | C -> T | NA |
LOC_Os11g24860.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g24860.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.721; most accessible tissue: Callus, score: 7.257 |
| vg1114174015 (J) | chr11 | 14174015 | C | T | 34.90% | 62.08% | C -> T | NA |
LOC_Os11g24860.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g24860.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.721; most accessible tissue: Callus, score: 7.257 |
| vg1114174182 (J) | chr11 | 14174182 | C | A | 35.60% | 60.16% | C -> T,A | NA |
LOC_Os11g24860.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g24860.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os11g24860.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.813; most accessible tissue: Callus, score: 19.270 |
| vg1114174187 (J) | chr11 | 14174187 | C | T | 35.40% | 60.22% | C -> T | NA |
LOC_Os11g24860.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g24860.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.813; most accessible tissue: Callus, score: 19.270 |