12 variations found. LOC_Os04g18230 (retrotransposon; putative; centromere-specific), ranging from 10,079,060 bp to 10,079,774 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0410079288 (J) | chr04 | 10079288 | C | T | 28.60% | 59.37% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g18230.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 5.017; most accessible tissue: Callus, score: 10.518 |
| vg0410079375 (J) | chr04 | 10079375 | C | A | 31.30% | 54.19% | C -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g18230.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0410079379 (J) | chr04 | 10079379 | A | G | 27.60% | 65.57% | A -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g18230.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0410079381 (J) | chr04 | 10079381 | T | A | 28.10% | 66.55% | T -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g18230.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0410079383 (J) | chr04 | 10079383 | T | A | 28.00% | 66.48% | T -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g18230.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0410079496 (J) | chr04 | 10079496 | C | Unkown | 20.60% | 72.70% | C -> T | NA |
LOC_Os04g18230.1 Alt: T| stop_gained HIGH(snpEff)
The average chromatin accessibility score: 4.479; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0410079688 (J) | chr04 | 10079688 | A | T | 20.90% | 62.38% | A -> T | NA |
LOC_Os04g18230.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g18230.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 7.066; most accessible tissue: Minghui63 panicle, score: 16.270 |
| vg0410079692 (J) | chr04 | 10079692 | G | A | 20.90% | 62.57% | G -> A | NA |
LOC_Os04g18230.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g18230.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 7.473; most accessible tissue: Minghui63 panicle, score: 16.270 |
| vg0410079705 (J) | chr04 | 10079705 | T | A | 21.10% | 62.04% | T -> A | NA |
LOC_Os04g18230.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g18230.1 Alt: A/stop_gained(CooVar) The average chromatin accessibility score: 8.657; most accessible tissue: Minghui63 panicle, score: 16.270 |
| vg0410079712 (J) | chr04 | 10079712 | T | C | 31.90% | 49.81% | T -> C | NA |
LOC_Os04g18230.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os04g18230.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 9.199; most accessible tissue: Minghui63 panicle, score: 16.270 |
| vg0410079763 (J) | chr04 | 10079763 | T | C | 29.60% | 62.78% | T -> C | NA |
LOC_Os04g18230.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os04g18230.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 12.886; most accessible tissue: Minghui63 panicle, score: 42.799 |
| vg0410079767 (J) | chr04 | 10079767 | G | C | 29.50% | 65.00% | G -> C | NA |
LOC_Os04g18230.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os04g18230.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 12.886; most accessible tissue: Minghui63 panicle, score: 42.799 |