14 variations found. LOC_Os01g64610 (retrotransposon protein; putative; unclassified; expressed), ranging from 37,497,517 bp to 37,500,819 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0137497667 (J) | chr01 | 37497667 | G | A | 31.50% | 66.72% | G -> A | NA |
LOC_Os01g64610.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os01g64610.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.856; most accessible tissue: Callus, score: 8.749 |
| vg0137498028 (J) | chr01 | 37498028 | C | T | 31.70% | 66.89% | C -> T | NA |
LOC_Os01g64610.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g64610.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.508; most accessible tissue: Callus, score: 15.917 |
| vg0137498663 (J) | chr01 | 37498663 | C | T | 34.60% | 63.16% | C -> T | NA |
LOC_Os01g64610.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g64610.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.646; most accessible tissue: Callus, score: 13.478 |
| vg0137499394 (J) | chr01 | 37499394 | G | A | 34.60% | 63.82% | G -> A | NA |
LOC_Os01g64610.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g64610.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.749; most accessible tissue: Minghui63 young leaf, score: 9.976 |
| vg0137499526 (J) | chr01 | 37499526 | T | A | 7.40% | 83.01% | T -> A | NA |
LOC_Os01g64600.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g64610.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 6.502; most accessible tissue: Callus, score: 16.181 |
| vg0137499575 (J) | chr01 | 37499575 | A | G | 29.00% | 65.30% | A -> G | NA |
LOC_Os01g64610.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g64610.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.502; most accessible tissue: Callus, score: 16.181 |
| vg0137499643 (J) | chr01 | 37499643 | A | G | 0.90% | 90.63% | A -> G | NA |
LOC_Os01g64610.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g64610.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.952; most accessible tissue: Callus, score: 12.634 |
| vg0137499722 (J) | chr01 | 37499722 | GC | G | 35.70% | 63.90% | GC -> G | NA |
LOC_Os01g64610.1 Alt: G| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os01g64610.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.370; most accessible tissue: Callus, score: 17.235 |
| vg0137499730 (J) | chr01 | 37499730 | G | A | 31.10% | 63.84% | G -> A | NA |
LOC_Os01g64610.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os01g64610.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.370; most accessible tissue: Callus, score: 17.235 |
| vg0137499770 (J) | chr01 | 37499770 | C | T | 35.90% | 63.27% | C -> T | NA |
LOC_Os01g64610.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g64610.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.035; most accessible tissue: Callus, score: 17.235 |
| vg0137499921 (J) | chr01 | 37499921 | A | G | 27.80% | 65.85% | A -> G | NA |
LOC_Os01g64610.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g64610.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.834; most accessible tissue: Callus, score: 8.507 |
| vg0137500132 (J) | chr01 | 37500132 | G | C | 32.40% | 63.58% | G -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g64600.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g64610.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0137500139 (J) | chr01 | 37500139 | C | T | 34.30% | 64.54% | C -> T | NA |
LOC_Os01g64600.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g64610.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0137500585 (J) | chr01 | 37500585 | G | A | 32.20% | 63.97% | G -> A | NA |
LOC_Os01g64610.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g64610.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |