11 variations found. LOC_Os09g09070 (retrotransposon protein; putative; unclassified; expressed), ranging from 4,847,029 bp to 4,848,437 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0904847226 (J) | chr09 | 4847226 | C | G | 23.00% | 73.59% | C -> G | NA |
LOC_Os09g09070.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os09g09070.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.451; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0904847583 (J) | chr09 | 4847583 | A | G | 17.30% | 77.00% | A -> G | NA |
LOC_Os09g09070.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os09g09070.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0904847587 (J) | chr09 | 4847587 | G | T | 21.10% | 76.32% | G -> T | NA |
LOC_Os09g09070.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g09070.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0904847618 (J) | chr09 | 4847618 | G | A | 23.30% | 73.59% | G -> A | NA |
LOC_Os09g09070.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g09070.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0904847664 (J) | chr09 | 4847664 | C | T | 20.20% | 74.63% | C -> T | NA |
LOC_Os09g09070.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g09070.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0904847668 (J) | chr09 | 4847668 | A | G | 19.60% | 75.10% | A -> G | NA |
LOC_Os09g09070.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os09g09070.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0904847977 (J) | chr09 | 4847977 | G | A | 17.20% | 79.20% | G -> A | NA |
LOC_Os09g09070.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g09070.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0904848027 (J) | chr09 | 4848027 | G | A | 16.90% | 79.62% | G -> A | NA |
LOC_Os09g09070.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g09070.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0904848030 (J) | chr09 | 4848030 | G | A | 16.70% | 79.64% | G -> A | NA |
LOC_Os09g09070.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g09070.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0904848031 (J) | chr09 | 4848031 | G | A | 14.30% | 82.42% | G -> A | NA |
LOC_Os09g09070.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g09070.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0904848203 (J) | chr09 | 4848203 | T | C | 14.00% | 84.15% | T -> C | NA |
LOC_Os09g09070.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g09070.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |