23 variations found. LOC_Os02g55830 (transposon protein; putative; unclassified; expressed), ranging from 34,178,560 bp to 34,180,696 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0234178688 (J) | chr02 | 34178688 | C | T | 33.40% | 47.95% | C -> T | NA |
LOC_Os02g55830.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g55830.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.041; most accessible tissue: Minghui63 panicle, score: 16.270 |
| vg0234178708 (J) | chr02 | 34178708 | G | A | 33.50% | 47.63% | G -> A | NA |
LOC_Os02g55830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g55830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os02g55830.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.041; most accessible tissue: Minghui63 panicle, score: 16.270 |
| vg0234178709 (J) | chr02 | 34178709 | G | A | 44.40% | 32.88% | G -> A | NA |
LOC_Os02g55830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g55830.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.041; most accessible tissue: Minghui63 panicle, score: 16.270 |
| vg0234178765 (J) | chr02 | 34178765 | G | T | 79.70% | 11.96% | G -> T | NA |
LOC_Os02g55830.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g55830.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.822; most accessible tissue: Minghui63 panicle, score: 16.270 |
| vg0234178772 (J) | chr02 | 34178772 | G | A | 78.30% | 14.56% | G -> A | NA |
LOC_Os02g55830.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os02g55830.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.822; most accessible tissue: Minghui63 panicle, score: 16.270 |
| vg0234178782 (J) | chr02 | 34178782 | C | T | 77.60% | 15.26% | C -> T | NA |
LOC_Os02g55830.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g55830.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.822; most accessible tissue: Minghui63 panicle, score: 16.270 |
| vg0234178793 (J) | chr02 | 34178793 | C | T | 76.10% | 16.34% | C -> T | NA |
LOC_Os02g55830.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g55830.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.822; most accessible tissue: Minghui63 panicle, score: 16.270 |
| vg0234179687 (J) | chr02 | 34179687 | A | G | 45.20% | 46.25% | A -> G | NA |
LOC_Os02g55840.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g55840.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.5 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.4 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.3 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.6 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55830.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.975; most accessible tissue: Callus, score: 10.052 |
| vg0234179766 (J) | chr02 | 34179766 | ACGTAAT G | A | 54.80% | 37.24% | ACGTAATG -> A | NA |
LOC_Os02g55840.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g55840.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.5 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.4 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.3 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.6 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55830.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.975; most accessible tissue: Callus, score: 10.052 |
| vg0234179772 (J) | chr02 | 34179772 | T | C | 53.60% | 39.34% | T -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os02g55840.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.5 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.4 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.3 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.6 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55830.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.975; most accessible tissue: Callus, score: 10.052 |
| vg0234179816 (J) | chr02 | 34179816 | C | G | 57.70% | 35.84% | C -> G | NA |
LOC_Os02g55840.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g55840.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.5 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.4 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.3 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.6 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55830.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.975; most accessible tissue: Callus, score: 10.052 |
| vg0234179817 (J) | chr02 | 34179817 | C | A | 46.40% | 35.38% | C -> A,T | NA |
LOC_Os02g55840.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g55840.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.5 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.4 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.3 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.6 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55830.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.5 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.4 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.3 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.6 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55830.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.975; most accessible tissue: Callus, score: 10.052 |
| vg0234179822 (J) | chr02 | 34179822 | A | G | 45.40% | 35.97% | A -> G | NA |
LOC_Os02g55840.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g55840.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.5 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.4 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.3 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.6 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55830.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.975; most accessible tissue: Callus, score: 10.052 |
| vg0234179855 (J) | chr02 | 34179855 | C | T | 54.20% | 39.04% | C -> T | NA |
LOC_Os02g55840.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g55840.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.5 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.4 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.3 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.6 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55830.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.505; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0234179980 (J) | chr02 | 34179980 | G | A | 20.80% | 56.75% | G -> A | NA |
LOC_Os02g55840.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g55840.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.5 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.4 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.3 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.6 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55830.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.505; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0234179994 (J) | chr02 | 34179994 | G | A | 43.30% | 49.17% | G -> A | NA |
LOC_Os02g55840.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g55840.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.5 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.4 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.3 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55840.6 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g55830.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 5.939; most accessible tissue: Minghui63 root, score: 10.708 |
| vg0234180290 (J) | chr02 | 34180290 | ATGGTGG | A | 45.10% | 51.61% | ATGGTGG -> A | NA |
LOC_Os02g55830.1 Alt: A| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os02g55830.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 9.274; most accessible tissue: Zhenshan97 root, score: 16.934 |
| vg0234180326 (J) | chr02 | 34180326 | AC | A | 71.70% | 16.42% | AC -> A | NA |
LOC_Os02g55830.1 Alt: A| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os02g55830.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 9.274; most accessible tissue: Zhenshan97 root, score: 16.934 |
| vg0234180328 (J) | chr02 | 34180328 | G | A | 71.40% | 16.46% | G -> A | NA |
LOC_Os02g55830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g55830.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 9.274; most accessible tissue: Zhenshan97 root, score: 16.934 |
| vg0234180503 (J) | chr02 | 34180503 | C | T | 51.90% | 42.81% | C -> T | NA |
LOC_Os02g55830.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os02g55830.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 8.338; most accessible tissue: Callus, score: 24.171 |
| vg0234180544 (J) | chr02 | 34180544 | A | T | 39.50% | 41.52% | A -> T | NA |
LOC_Os02g55830.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g55830.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 7.023; most accessible tissue: Callus, score: 24.171 |
| vg0234180603 (J) | chr02 | 34180603 | A | G | 38.80% | 43.84% | A -> G | NA |
LOC_Os02g55830.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g55830.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.244; most accessible tissue: Callus, score: 15.598 |
| vg0234180608 (J) | chr02 | 34180608 | C | T | 46.40% | 47.59% | C -> T | NA |
LOC_Os02g55830.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g55830.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.114; most accessible tissue: Callus, score: 15.598 |