12 variations found. LOC_Os10g15100 (retrotransposon protein; putative; unclassified), ranging from 7,912,242 bp to 7,913,251 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1007912248 (J) | chr10 | 7912248 | A | G | 98.70% | 0.89% | A -> G | NA |
LOC_Os10g15100.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g15100.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 10.836; most accessible tissue: Zhenshan97 flag leaf, score: 18.943 |
| vg1007912254 (J) | chr10 | 7912254 | C | T | 99.10% | 0.89% | C -> T | NA |
LOC_Os10g15100.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g15100.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 12.485; most accessible tissue: Zhenshan97 flag leaf, score: 23.298 |
| vg1007912256 (J) | chr10 | 7912256 | G | C | 98.80% | 0.89% | G -> C | NA |
LOC_Os10g15100.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os10g15100.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 12.485; most accessible tissue: Zhenshan97 flag leaf, score: 23.298 |
| vg1007912258 (J) | chr10 | 7912258 | G | A | 99.00% | 0.89% | G -> A | NA |
LOC_Os10g15100.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g15100.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 12.485; most accessible tissue: Zhenshan97 flag leaf, score: 23.298 |
| vg1007912269 (J) | chr10 | 7912269 | G | A | 94.70% | 3.03% | G -> A | NA |
LOC_Os10g15100.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g15100.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 15.487; most accessible tissue: Zhenshan97 flag leaf, score: 26.688 |
| vg1007912385 (J) | chr10 | 7912385 | T | C | 16.90% | 71.77% | T -> C | NA |
LOC_Os10g15100.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g15100.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 17.755; most accessible tissue: Zhenshan97 root, score: 30.989 |
| vg1007912486 (J) | chr10 | 7912486 | C | T | 12.40% | 40.86% | C -> T | NA |
LOC_Os10g15100.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 24.931; most accessible tissue: Zhenshan97 flag leaf, score: 48.165 |
| vg1007912549 (J) | chr10 | 7912549 | C | T | 43.90% | 9.48% | C -> T | NA |
LOC_Os10g15100.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 24.853; most accessible tissue: Zhenshan97 root, score: 47.644 |
| vg1007912566 (J) | chr10 | 7912566 | T | C | 98.70% | 0.95% | T -> C | NA |
LOC_Os10g15100.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 24.853; most accessible tissue: Zhenshan97 root, score: 47.644 |
| vg1007912745 (J) | chr10 | 7912745 | A | G | 15.50% | 78.95% | A -> G | NA |
LOC_Os10g15100.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 16.787; most accessible tissue: Zhenshan97 root, score: 29.203 |
| vg1007912801 (J) | chr10 | 7912801 | T | C | 17.80% | 44.54% | T -> C | NA |
LOC_Os10g15100.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 11.874; most accessible tissue: Zhenshan97 root, score: 18.731 |
| vg1007913125 (J) | chr10 | 7913125 | C | T | 14.50% | 48.90% | C -> T | NA |
LOC_Os10g15100.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 8.455; most accessible tissue: Minghui63 panicle, score: 25.313 |