17 variations found. LOC_Os02g38530 (retrotransposon protein; putative; unclassified), ranging from 23,298,444 bp to 23,298,860 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0223298450 (J) | chr02 | 23298450 | A | G | 33.50% | 55.99% | A -> G | NA |
LOC_Os02g38530.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g38530.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.429; most accessible tissue: Zhenshan97 flag leaf, score: 9.474 |
| vg0223298462 (J) | chr02 | 23298462 | A | C | 22.80% | 63.22% | A -> C | NA |
LOC_Os02g38530.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g38530.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 5.820; most accessible tissue: Zhenshan97 flag leaf, score: 9.474 |
| vg0223298478 (J) | chr02 | 23298478 | A | G | 18.10% | 68.75% | A -> G | NA |
LOC_Os02g38530.1 Alt: G| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os02g38540.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38520.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 5.820; most accessible tissue: Zhenshan97 flag leaf, score: 9.474 |
| vg0223298487 (J) | chr02 | 23298487 | A | G | 19.40% | 65.76% | A -> G | NA |
LOC_Os02g38540.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g38520.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38530.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 5.820; most accessible tissue: Zhenshan97 flag leaf, score: 9.474 |
| vg0223298502 (J) | chr02 | 23298502 | A | G | 16.90% | 74.93% | A -> G | NA |
LOC_Os02g38540.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g38520.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38530.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 5.820; most accessible tissue: Zhenshan97 flag leaf, score: 9.474 |
| vg0223298543 (J) | chr02 | 23298543 | T | C | 17.20% | 67.41% | T -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os02g38540.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38520.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38530.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 5.820; most accessible tissue: Zhenshan97 flag leaf, score: 9.474 |
| vg0223298575 (J) | chr02 | 23298575 | A | G | 24.00% | 58.32% | A -> G | NA |
LOC_Os02g38540.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g38520.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38530.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 5.820; most accessible tissue: Zhenshan97 flag leaf, score: 9.474 |
| vg0223298581 (J) | chr02 | 23298581 | G | T | 40.10% | 50.32% | G -> T | NA |
LOC_Os02g38540.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g38520.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38530.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 5.523; most accessible tissue: Zhenshan97 flag leaf, score: 9.474 |
| vg0223298586 (J) | chr02 | 23298586 | A | G | 40.20% | 50.28% | A -> G | NA |
LOC_Os02g38540.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g38520.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38530.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 5.523; most accessible tissue: Zhenshan97 flag leaf, score: 9.474 |
| vg0223298592 (J) | chr02 | 23298592 | T | A | 42.60% | 50.25% | T -> A | NA |
LOC_Os02g38540.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g38520.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38530.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 5.523; most accessible tissue: Zhenshan97 flag leaf, score: 9.474 |
| vg0223298666 (J) | chr02 | 23298666 | A | G | 19.60% | 65.64% | A -> G | NA |
LOC_Os02g38540.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g38520.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38530.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 5.759; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 |
| vg0223298690 (J) | chr02 | 23298690 | T | A | 27.10% | 54.85% | T -> A | NA |
LOC_Os02g38530.1 Alt: A| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os02g38540.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38520.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 5.759; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 |
| vg0223298777 (J) | chr02 | 23298777 | C | T | 5.10% | 58.19% | C -> T | NA |
LOC_Os02g38530.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g38530.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.953; most accessible tissue: Minghui63 flower, score: 10.335 |
| vg0223298793 (J) | chr02 | 23298793 | C | T | 65.80% | 17.73% | C -> T | NA |
LOC_Os02g38530.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g38530.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.953; most accessible tissue: Minghui63 flower, score: 10.335 |
| vg0223298801 (J) | chr02 | 23298801 | T | C | 66.60% | 17.41% | T -> C | NA |
LOC_Os02g38530.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g38530.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 6.071; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 |
| vg0223298802 (J) | chr02 | 23298802 | T | C | 60.00% | 17.12% | T -> C | NA |
LOC_Os02g38530.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g38530.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 6.071; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 |
| vg0223298809 (J) | chr02 | 23298809 | C | A | 68.30% | 16.21% | C -> A | NA |
LOC_Os02g38530.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g38530.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.159; most accessible tissue: Zhenshan97 flag leaf, score: 11.736 |