11 variations found. LOC_Os08g23760 (retrotransposon protein; putative; unclassified; expressed), ranging from 14,379,882 bp to 14,383,110 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0814380086 (J) | chr08 | 14380086 | C | T | 23.60% | 59.75% | C -> T | NA |
LOC_Os08g23760.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g23760.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 13.775; most accessible tissue: Zhenshan97 root, score: 27.411 |
| vg0814380143 (J) | chr08 | 14380143 | G | T | 19.20% | 78.67% | G -> T | NA |
LOC_Os08g23760.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g23760.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 14.258; most accessible tissue: Zhenshan97 root, score: 27.411 |
| vg0814380312 (J) | chr08 | 14380312 | C | T | 0.20% | 97.27% | T -> C | NA |
LOC_Os08g23760.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g23760.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 13.423; most accessible tissue: Minghui63 young leaf, score: 23.613 |
| vg0814380656 (J) | chr08 | 14380656 | T | C | 0.20% | 94.14% | C -> T | NA |
LOC_Os08g23760.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g23760.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.207; most accessible tissue: Minghui63 flower, score: 7.958 |
| vg0814380695 (J) | chr08 | 14380695 | C | Unkown | 0.20% | 93.46% | T -> C | NA |
LOC_Os08g23760.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g23760.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.207; most accessible tissue: Minghui63 flower, score: 7.958 |
| vg0814381584 (J) | chr08 | 14381584 | G | A | 1.70% | 95.87% | G -> A | NA |
LOC_Os08g23760.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os08g23760.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 25.733; most accessible tissue: Minghui63 panicle, score: 50.413 |
| vg0814381605 (J) | chr08 | 14381605 | G | A | 1.40% | 95.70% | G -> A | NA |
LOC_Os08g23760.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os08g23760.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 25.733; most accessible tissue: Minghui63 panicle, score: 50.413 |
| vg0814381647 (J) | chr08 | 14381647 | A | G | 0.80% | 96.80% | A -> G | NA |
LOC_Os08g23760.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os08g23760.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 25.733; most accessible tissue: Minghui63 panicle, score: 50.413 |
| vg0814381652 (J) | chr08 | 14381652 | C | T | 1.00% | 96.19% | C -> T | NA |
LOC_Os08g23760.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g23760.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 25.733; most accessible tissue: Minghui63 panicle, score: 50.413 |
| vg0814383017 (J) | chr08 | 14383017 | G | A | 37.30% | 44.18% | G -> A | NA |
LOC_Os08g23760.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g23760.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.318; most accessible tissue: Zhenshan97 flag leaf, score: 7.948 |
| vg0814383064 (J) | chr08 | 14383064 | G | C | 19.10% | 76.58% | G -> C | NA |
LOC_Os08g23760.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g23760.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.318; most accessible tissue: Zhenshan97 flag leaf, score: 7.948 |