33 variations found. LOC_Os02g35800 (retrotransposon protein; putative; unclassified; expressed), ranging from 21,508,662 bp to 21,511,292 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0221508689 (J) | chr02 | 21508689 | C | T | 36.00% | 63.25% | C -> T | NA |
LOC_Os02g35800.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g35800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 12.038; most accessible tissue: Callus, score: 31.066 |
| vg0221508703 (J) | chr02 | 21508703 | T | TTAG | 36.60% | 61.76% | T -> TTAG | NA |
LOC_Os02g35800.1 Alt: TTAG| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os02g35800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 12.241; most accessible tissue: Callus, score: 31.066 |
| vg0221508931 (J) | chr02 | 21508931 | G | A | 36.30% | 60.20% | G -> A | NA |
LOC_Os02g35800.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g35800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 11.107; most accessible tissue: Callus, score: 25.550 |
| vg0221509038 (J) | chr02 | 21509038 | T | C | 35.30% | 64.07% | T -> C | NA |
LOC_Os02g35800.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g35800.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 10.913; most accessible tissue: Callus, score: 25.550 |
| vg0221509060 (J) | chr02 | 21509060 | G | A | 35.40% | 63.80% | G -> A | NA |
LOC_Os02g35800.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os02g35800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 10.345; most accessible tissue: Callus, score: 25.550 |
| vg0221509073 (J) | chr02 | 21509073 | C | T | 35.30% | 64.01% | C -> T | NA |
LOC_Os02g35800.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g35800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 10.207; most accessible tissue: Callus, score: 25.550 |
| vg0221509074 (J) | chr02 | 21509074 | G | C | 35.30% | 64.05% | G -> C | NA |
LOC_Os02g35800.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g35800.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 10.207; most accessible tissue: Callus, score: 25.550 |
| vg0221509081 (J) | chr02 | 21509081 | T | C | 35.20% | 64.07% | T -> C | NA |
LOC_Os02g35800.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g35800.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 8.891; most accessible tissue: Minghui63 panicle, score: 16.270 |
| vg0221509088 (J) | chr02 | 21509088 | A | G | 35.20% | 64.13% | A -> G | NA |
LOC_Os02g35800.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g35800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 8.891; most accessible tissue: Minghui63 panicle, score: 16.270 |
| vg0221509093 (J) | chr02 | 21509093 | G | A | 35.50% | 63.94% | G -> A | NA |
LOC_Os02g35800.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g35800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 8.891; most accessible tissue: Minghui63 panicle, score: 16.270 |
| vg0221509286 (J) | chr02 | 21509286 | G | T | 34.90% | 62.70% | G -> T | NA |
LOC_Os02g35800.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g35800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.563; most accessible tissue: Callus, score: 14.511 |
| vg0221509287 (J) | chr02 | 21509287 | G | T | 34.80% | 62.82% | G -> T | NA |
LOC_Os02g35800.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g35800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.563; most accessible tissue: Callus, score: 14.511 |
| vg0221509541 (J) | chr02 | 21509541 | C | T | 34.80% | 64.16% | C -> T | NA |
LOC_Os02g35800.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g35800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.787; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0221509608 (J) | chr02 | 21509608 | T | C | 36.30% | 55.27% | T -> C | NA |
LOC_Os02g35800.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g35800.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 4.785; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0221509625 (J) | chr02 | 21509625 | G | A | 40.80% | 52.05% | G -> A | NA |
LOC_Os02g35800.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g35800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.785; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0221509629 (J) | chr02 | 21509629 | C | T | 40.60% | 52.29% | C -> T | NA |
LOC_Os02g35800.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g35800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.785; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0221509631 (J) | chr02 | 21509631 | G | A | 43.00% | 50.51% | G -> A | NA |
LOC_Os02g35800.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g35800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.785; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0221509787 (J) | chr02 | 21509787 | C | T | 33.60% | 63.69% | C -> T | NA |
LOC_Os02g35800.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g35800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.501; most accessible tissue: Minghui63 root, score: 13.235 |
| vg0221509916 (J) | chr02 | 21509916 | G | A | 34.80% | 63.77% | G -> A | NA |
LOC_Os02g35800.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g35800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.195; most accessible tissue: Minghui63 root, score: 13.235 |
| vg0221509991 (J) | chr02 | 21509991 | A | G | 40.20% | 53.05% | A -> G | NA |
LOC_Os02g35780.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g35790.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35810.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35800.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 6.528; most accessible tissue: Minghui63 root, score: 13.235 |
| vg0221509995 (J) | chr02 | 21509995 | G | A | 41.00% | 51.67% | G -> A | NA |
LOC_Os02g35780.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g35790.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35810.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35800.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 6.528; most accessible tissue: Minghui63 root, score: 13.235 |
| vg0221510031 (J) | chr02 | 21510031 | G | A | 39.60% | 52.41% | G -> A | NA |
LOC_Os02g35800.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g35800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.528; most accessible tissue: Minghui63 root, score: 13.235 |
| vg0221510153 (J) | chr02 | 21510153 | G | A | 33.70% | 63.61% | G -> A | NA |
LOC_Os02g35800.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g35800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.451; most accessible tissue: Minghui63 root, score: 15.664 |
| vg0221510339 (J) | chr02 | 21510339 | G | A | 25.30% | 64.49% | G -> A | NA |
LOC_Os02g35780.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g35790.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35810.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35800.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 7.886; most accessible tissue: Minghui63 root, score: 21.615 |
| vg0221510347 (J) | chr02 | 21510347 | T | A | 35.20% | 64.56% | T -> A | NA |
LOC_Os02g35780.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g35790.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35810.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35800.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 7.969; most accessible tissue: Minghui63 root, score: 21.615 |
| vg0221510356 (J) | chr02 | 21510356 | A | G | 35.00% | 64.71% | A -> G | NA |
LOC_Os02g35780.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g35790.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35810.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35800.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 7.969; most accessible tissue: Minghui63 root, score: 21.615 |
| vg0221510366 (J) | chr02 | 21510366 | G | A | 35.10% | 64.64% | G -> A | NA |
LOC_Os02g35780.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g35790.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35810.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35800.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 7.969; most accessible tissue: Minghui63 root, score: 21.615 |
| vg0221510372 (J) | chr02 | 21510372 | G | A | 35.10% | 64.64% | G -> A | NA |
LOC_Os02g35780.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g35790.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35810.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35800.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 7.969; most accessible tissue: Minghui63 root, score: 21.615 |
| vg0221510713 (J) | chr02 | 21510713 | G | A | 35.80% | 60.28% | G -> A | NA |
LOC_Os02g35800.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g35800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 13.877; most accessible tissue: Minghui63 panicle, score: 46.754 |
| vg0221510773 (J) | chr02 | 21510773 | TG | T | 34.80% | 63.94% | TG -> T | NA |
LOC_Os02g35800.1 Alt: T| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os02g35800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 13.691; most accessible tissue: Minghui63 panicle, score: 46.754 |
| vg0221511044 (J) | chr02 | 21511044 | C | T | 35.50% | 63.27% | C -> T | NA |
LOC_Os02g35800.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os02g35800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.322; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg0221511095 (J) | chr02 | 21511095 | T | C | 35.70% | 63.20% | T -> C | NA |
LOC_Os02g35800.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g35800.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 6.464; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg0221511103 (J) | chr02 | 21511103 | A | G | 35.70% | 63.03% | A -> G | NA |
LOC_Os02g35800.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g35800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.464; most accessible tissue: Zhenshan97 panicle, score: 16.188 |