11 variations found. LOC_Os01g72070 (retrotransposon protein; putative; unclassified; expressed), ranging from 41,808,512 bp to 41,809,571 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0141808872 (J) | chr01 | 41808872 | T | C | 27.80% | 67.10% | T -> C | NA |
LOC_Os01g72070.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g72070.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 4.998; most accessible tissue: Callus, score: 10.303 |
| vg0141809107 (J) | chr01 | 41809107 | G | A | 5.10% | 81.61% | G -> A | NA |
LOC_Os01g72070.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g72070.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.016; most accessible tissue: Callus, score: 10.504 |
| vg0141809199 (J) | chr01 | 41809199 | G | A | 27.50% | 68.32% | G -> A | NA |
LOC_Os01g72070.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os01g72070.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.279; most accessible tissue: Callus, score: 13.399 |
| vg0141809216 (J) | chr01 | 41809216 | C | A | 18.10% | 76.89% | C -> A | NA |
LOC_Os01g72070.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g72070.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.279; most accessible tissue: Callus, score: 13.399 |
| vg0141809230 (J) | chr01 | 41809230 | C | T | 28.30% | 66.57% | C -> T | NA |
LOC_Os01g72070.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g72070.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.279; most accessible tissue: Callus, score: 13.399 |
| vg0141809239 (J) | chr01 | 41809239 | G | A | 28.20% | 66.99% | G -> A | NA |
LOC_Os01g72070.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g72070.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.279; most accessible tissue: Callus, score: 13.399 |
| vg0141809260 (J) | chr01 | 41809260 | G | A | 27.40% | 67.41% | G -> A | NA |
LOC_Os01g72070.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g72070.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.279; most accessible tissue: Callus, score: 13.399 |
| vg0141809326 (J) | chr01 | 41809326 | G | A | 17.60% | 80.79% | G -> A | NA |
LOC_Os01g72070.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g72070.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.668; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0141809389 (J) | chr01 | 41809389 | C | T | 17.90% | 79.20% | C -> T | NA |
LOC_Os01g72070.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g72070.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.668; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0141809446 (J) | chr01 | 41809446 | C | T | 12.70% | 82.33% | T -> C | NA |
LOC_Os01g72070.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g72070.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 5.092; most accessible tissue: Callus, score: 11.339 |
| vg0141809508 (J) | chr01 | 41809508 | G | A | 15.00% | 81.15% | G -> A | NA |
LOC_Os01g72070.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os01g72070.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.275; most accessible tissue: Callus, score: 11.339 |