9 variations found. LOC_Os09g13850 (retrotransposon protein; putative; unclassified; expressed), ranging from 8,137,159 bp to 8,138,557 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0908137180 (J) | chr09 | 8137180 | G | A | 48.60% | 44.29% | G -> A | NA |
LOC_Os09g13850.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g13850.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 19.361; most accessible tissue: Minghui63 panicle, score: 50.413 |
| vg0908137189 (J) | chr09 | 8137189 | C | T | 48.50% | 44.33% | C -> T | NA |
LOC_Os09g13850.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g13850.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 19.415; most accessible tissue: Minghui63 panicle, score: 46.754 |
| vg0908137198 (J) | chr09 | 8137198 | T | C | 48.50% | 42.78% | T -> C | NA |
LOC_Os09g13850.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g13850.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 19.879; most accessible tissue: Minghui63 panicle, score: 46.754 |
| vg0908137199 (J) | chr09 | 8137199 | G | A | 53.10% | 38.85% | G -> A | NA |
LOC_Os09g13850.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g13850.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 20.001; most accessible tissue: Minghui63 panicle, score: 46.754 |
| vg0908137347 (J) | chr09 | 8137347 | G | A | 41.90% | 50.83% | G -> A | NA |
LOC_Os09g13850.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g13850.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 25.698; most accessible tissue: Minghui63 flag leaf, score: 54.348 |
| vg0908137400 (J) | chr09 | 8137400 | G | A | 41.00% | 52.90% | G -> A | NA |
LOC_Os09g13850.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g13850.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 28.376; most accessible tissue: Minghui63 flag leaf, score: 61.847 |
| vg0908137531 (J) | chr09 | 8137531 | G | A | 38.90% | 55.14% | G -> A | NA |
LOC_Os09g13850.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g13850.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 28.621; most accessible tissue: Minghui63 flag leaf, score: 61.214 |
| vg0908137676 (J) | chr09 | 8137676 | G | A | 39.80% | 53.39% | G -> A | NA |
LOC_Os09g13850.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g13850.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 26.256; most accessible tissue: Minghui63 panicle, score: 59.629 |
| vg0908138309 (J) | chr09 | 8138309 | C | G | 40.80% | 40.39% | C -> G | NA |
LOC_Os09g13850.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os09g13850.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 28.070; most accessible tissue: Minghui63 panicle, score: 66.554 |