25 variations found. LOC_Os02g38040 (leucine-rich repeat family protein; putative; expressed), ranging from 22,978,829 bp to 22,981,571 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0222978874 (J) | chr02 | 22978874 | CCTCTCT CT | CCT | 85.40% | 1.04% | CCTCTCTCT -> CCTCTCTCTC T,CCTCTCT, CCT,CCTCTC TCTCTCTCT, C,CCTCTCTC TCTCT | NA |
LOC_Os02g38040.1 Alt: CCTCTCTCTCTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g38029.1 Alt: CCTCTCTCTCTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38020.1 Alt: CCTCTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.1 Alt: CCTCTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38020.2 Alt: CCTCTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.4 Alt: CCTCTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.3 Alt: CCTCTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.5 Alt: CCTCTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.6 Alt: CCTCTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.2 Alt: CCTCTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38040.1 Alt: CCTCTCTCTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38029.1 Alt: CCTCTCTCTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38020.1 Alt: CCTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.1 Alt: CCTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38020.2 Alt: CCTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.4 Alt: CCTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.3 Alt: CCTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.5 Alt: CCTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.6 Alt: CCTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.2 Alt: CCTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38040.1 Alt: CCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38029.1 Alt: CCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38020.1 Alt: CCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.1 Alt: CCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38020.2 Alt: CCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.4 Alt: CCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.3 Alt: CCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.5 Alt: CCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.6 Alt: CCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.2 Alt: CCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os02g38040.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38029.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38020.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38020.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.4 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.5 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.6 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38040.1 Alt: CCTCTCTCTCTCTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38029.1 Alt: CCTCTCTCTCTCTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38020.1 Alt: CCTCTCTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.1 Alt: CCTCTCTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38020.2 Alt: CCTCTCTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.4 Alt: CCTCTCTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.3 Alt: CCTCTCTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.5 Alt: CCTCTCTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.6 Alt: CCTCTCTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.2 Alt: CCTCTCTCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38040.1 Alt: CCTCTCT| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os02g38029.1 Alt: CCTCTCT| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g38020.1 Alt: CCTCTCT| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g38050.1 Alt: CCTCTCT| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g38020.2 Alt: CCTCTCT| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g38050.4 Alt: CCTCTCT| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g38050.3 Alt: CCTCTCT| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g38050.5 Alt: CCTCTCT| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g38050.6 Alt: CCTCTCT| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g38050.2 Alt: CCTCTCT| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 92.404; most accessible tissue: Zhenshan97 flag leaf, score: 95.641 |
| vg0222978950 (J) | chr02 | 22978950 | G | T | 99.00% | 0.00% | G -> T | NA |
LOC_Os02g38040.1 Alt: T| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os02g38040.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38029.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38020.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38020.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.4 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.5 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.6 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 92.976; most accessible tissue: Zhenshan97 flag leaf, score: 95.466 |
| vg0222979271 (J) | chr02 | 22979271 | C | T | 99.00% | 0.00% | C -> T | NA |
LOC_Os02g38040.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 88.513; most accessible tissue: Zhenshan97 flag leaf, score: 94.128 |
| vg0222979456 (J) | chr02 | 22979456 | G | A | 96.60% | 0.00% | G -> A | NA |
LOC_Os02g38040.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 85.137; most accessible tissue: Zhenshan97 flag leaf, score: 92.620 |
| vg0222979619 (J) | chr02 | 22979619 | C | T | 96.60% | 0.00% | C -> T | NA |
LOC_Os02g38040.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 77.244; most accessible tissue: Zhenshan97 flag leaf, score: 88.918 |
| vg0222979709 (J) | chr02 | 22979709 | AT | A | 99.60% | 0.00% | AT -> A | NA |
LOC_Os02g38029.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g38020.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38020.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.4 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.5 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.6 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38040.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 72.310; most accessible tissue: Callus, score: 87.432 |
| vg0222979755 (J) | chr02 | 22979755 | C | G | 95.50% | 0.00% | C -> G | NA |
LOC_Os02g38029.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g38020.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38020.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.4 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.5 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.6 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38040.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.605; most accessible tissue: Callus, score: 87.432 |
| vg0222979913 (J) | chr02 | 22979913 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os02g38029.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os02g38020.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g38050.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g38020.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g38050.4 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g38050.3 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g38050.5 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g38050.6 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g38050.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g38040.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 56.315; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 |
| vg0222979993 (J) | chr02 | 22979993 | ATT | AT | 85.30% | 0.53% | ATT -> ATTT,AT,A, TTT | NA |
LOC_Os02g38029.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g38020.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38020.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.4 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.5 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.6 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38040.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os02g38029.1 Alt: ATTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38020.1 Alt: ATTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.1 Alt: ATTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38020.2 Alt: ATTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.4 Alt: ATTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.3 Alt: ATTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.5 Alt: ATTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.6 Alt: ATTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.2 Alt: ATTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38040.1 Alt: ATTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38029.1 Alt: TTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38020.1 Alt: TTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.1 Alt: TTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38020.2 Alt: TTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.4 Alt: TTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.3 Alt: TTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.5 Alt: TTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.6 Alt: TTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.2 Alt: TTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38040.1 Alt: TTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38029.1 Alt: AT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38020.1 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.1 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38020.2 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.4 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.3 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.5 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.6 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.2 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38040.1 Alt: AT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 55.890; most accessible tissue: Callus, score: 82.461 |
| vg0222980080 (J) | chr02 | 22980080 | G | T | 96.20% | 0.00% | G -> T | NA |
LOC_Os02g38029.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g38020.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38020.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.4 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.5 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.6 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38040.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 47.489; most accessible tissue: Zhenshan97 flag leaf, score: 64.768 |
| vg0222980308 (J) | chr02 | 22980308 | G | C | 98.30% | 0.00% | G -> C | NA |
LOC_Os02g38040.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 72.722; most accessible tissue: Callus, score: 81.261 |
| vg0222980338 (J) | chr02 | 22980338 | G | A | 99.60% | 0.00% | G -> A | NA |
LOC_Os02g38040.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 71.943; most accessible tissue: Zhenshan97 flag leaf, score: 80.373 |
| vg0222980378 (J) | chr02 | 22980378 | A | G | 96.60% | 0.00% | A -> G | NA |
LOC_Os02g38040.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 71.913; most accessible tissue: Zhenshan97 flag leaf, score: 81.605 |
| vg0222980452 (J) | chr02 | 22980452 | G | A | 99.50% | 0.00% | G -> A | NA |
LOC_Os02g38029.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os02g38050.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g38050.4 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g38050.3 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g38050.5 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g38050.6 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g38050.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g38040.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 79.798; most accessible tissue: Callus, score: 87.013 |
| vg0222980472 (J) | chr02 | 22980472 | C | T | 96.70% | 0.00% | C -> T | NA |
LOC_Os02g38029.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g38050.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.4 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.5 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.6 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38040.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 81.770; most accessible tissue: Callus, score: 87.013 |
| vg0222980479 (J) | chr02 | 22980479 | A | T | 96.10% | 0.00% | A -> T | NA |
LOC_Os02g38029.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g38050.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.4 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.5 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.6 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38040.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 81.827; most accessible tissue: Callus, score: 87.013 |
| vg0222980482 (J) | chr02 | 22980482 | T | G | 99.80% | 0.00% | T -> G,A | NA |
LOC_Os02g38029.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os02g38050.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g38050.4 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g38050.3 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g38050.5 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g38050.6 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g38050.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g38040.1 Alt: A| intron_variant MODIFIER(snpEff) LOC_Os02g38029.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g38050.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g38050.4 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g38050.3 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g38050.5 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g38050.6 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g38050.2 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g38040.1 Alt: G| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 81.927; most accessible tissue: Callus, score: 87.013 |
| vg0222981020 (J) | chr02 | 22981020 | G | A | 99.00% | 0.00% | G -> A | NA |
LOC_Os02g38040.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 92.214; most accessible tissue: Minghui63 root, score: 95.636 |
| vg0222981032 (J) | chr02 | 22981032 | C | T | 95.40% | 0.00% | C -> T | NA |
LOC_Os02g38040.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 92.184; most accessible tissue: Minghui63 root, score: 95.647 |
| vg0222981184 (J) | chr02 | 22981184 | A | G | 96.10% | 0.00% | A -> G | NA |
LOC_Os02g38040.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 91.321; most accessible tissue: Minghui63 root, score: 95.261 |
| vg0222981332 (J) | chr02 | 22981332 | TTG | T | 99.00% | 0.00% | TTG -> T | NA |
LOC_Os02g38040.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g38029.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.4 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.5 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.6 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 85.895; most accessible tissue: Minghui63 root, score: 93.779 |
| vg0222981421 (J) | chr02 | 22981421 | C | CAGG | 96.70% | 0.00% | C -> CAGG | NA |
LOC_Os02g38040.1 Alt: CAGG| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g38029.1 Alt: CAGG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.1 Alt: CAGG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.4 Alt: CAGG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.3 Alt: CAGG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.5 Alt: CAGG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.6 Alt: CAGG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.2 Alt: CAGG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 83.155; most accessible tissue: Minghui63 root, score: 92.642 |
| vg0222981442 (J) | chr02 | 22981442 | CTG | C | 96.70% | 0.00% | CTG -> C | NA |
LOC_Os02g38040.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g38029.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.4 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.5 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.6 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 84.599; most accessible tissue: Callus, score: 95.364 |
| vg0222981540 (J) | chr02 | 22981540 | G | T | 96.60% | 0.00% | G -> T | NA |
LOC_Os02g38040.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g38029.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.4 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.5 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.6 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 82.699; most accessible tissue: Callus, score: 95.364 |
| vg0222981570 (J) | chr02 | 22981570 | T | A | 96.60% | 0.00% | T -> A | NA |
LOC_Os02g38040.1 Alt: A| splice_region_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os02g38040.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38029.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.4 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.5 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.6 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g38050.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 83.515; most accessible tissue: Callus, score: 95.364 |