36 variations found. LOC_Os02g06640 (ubiquitin family protein; putative; expressed), ranging from 3,340,310 bp to 3,343,062 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 |
|---|---|---|---|---|---|---|---|---|---|
| STR0203343061 (J) | chr02 | 3343061 | GAGGAGA GGAGA | GAGGAGA GGAGAGG A | 98.10% | 0.00% | GAGGAGAGGA GA -> GAGGAGAGGA GAGGA | NA |
|
| vg0203340405 (J) | chr02 | 3340405 | A | G | 79.00% | 0.00% | G -> A | NA |
LOC_Os02g06640.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06640.4 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g06640.3 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g06630.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g06650.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 93.799; most accessible tissue: Zhenshan97 young leaf, score: 99.139 |
| vg0203340416 (J) | chr02 | 3340416 | A | G | 99.30% | 0.00% | A -> G | NA |
LOC_Os02g06640.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06640.4 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g06640.3 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g06630.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g06650.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 93.567; most accessible tissue: Zhenshan97 young leaf, score: 99.111 |
| vg0203340494 (J) | chr02 | 3340494 | TC | T | 99.30% | 0.00% | TC -> T | NA |
LOC_Os02g06640.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06640.4 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g06640.3 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g06630.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g06650.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 95.505; most accessible tissue: Zhenshan97 young leaf, score: 99.312 |
| vg0203340534 (J) | chr02 | 3340534 | G | A | 94.60% | 0.00% | G -> A | NA |
LOC_Os02g06640.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06640.4 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g06640.3 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g06630.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g06650.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 95.895; most accessible tissue: Zhenshan97 young leaf, score: 99.349 |
| vg0203340607 (J) | chr02 | 3340607 | T | C | 78.90% | 0.28% | C -> T | NA |
LOC_Os02g06640.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06640.4 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g06640.3 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g06630.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g06650.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 95.910; most accessible tissue: Zhenshan97 young leaf, score: 99.491 |
| vg0203340671 (J) | chr02 | 3340671 | C | A | 99.80% | 0.00% | C -> A | NA |
LOC_Os02g06640.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os02g06640.4 Alt: A| synonymous_variant LOW(snpEff) LOC_Os02g06640.3 Alt: A| synonymous_variant LOW(snpEff) LOC_Os02g06630.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g06650.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 96.266; most accessible tissue: Zhenshan97 young leaf, score: 99.562 |
| vg0203340749 (J) | chr02 | 3340749 | C | G | 99.90% | 0.00% | C -> G | NA |
LOC_Os02g06640.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os02g06640.4 Alt: G| synonymous_variant LOW(snpEff) LOC_Os02g06640.3 Alt: G| synonymous_variant LOW(snpEff) LOC_Os02g06630.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g06650.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 97.110; most accessible tissue: Zhenshan97 young leaf, score: 99.628 |
| vg0203340866 (J) | chr02 | 3340866 | G | A | 98.90% | 0.00% | G -> A | NA |
LOC_Os02g06640.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g06640.4 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os02g06640.3 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 94.094; most accessible tissue: Zhenshan97 young leaf, score: 99.596 |
| vg0203340938 (J) | chr02 | 3340938 | A | G | 78.80% | 0.06% | G -> A | NA |
LOC_Os02g06640.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g06640.4 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os02g06640.3 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os02g06640.3 Alt: DEL/frameshift_variant(CooVar) LOC_Os02g06640.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os02g06640.4 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 95.662; most accessible tissue: Zhenshan97 young leaf, score: 99.566 |
| vg0203340968 (J) | chr02 | 3340968 | G | A | 94.40% | 0.00% | G -> A | NA |
LOC_Os02g06640.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g06640.4 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os02g06640.3 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 95.539; most accessible tissue: Zhenshan97 young leaf, score: 99.545 |
| vg0203341217 (J) | chr02 | 3341217 | G | A | 99.30% | 0.00% | G -> A | NA |
LOC_Os02g06640.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g06640.4 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 95.440; most accessible tissue: Zhenshan97 young leaf, score: 99.437 |
| vg0203341307 (J) | chr02 | 3341307 | G | A | 94.60% | 0.00% | G -> A | NA |
LOC_Os02g06640.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g06640.4 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 94.945; most accessible tissue: Zhenshan97 young leaf, score: 99.356 |
| vg0203341322 (J) | chr02 | 3341322 | G | A | 99.30% | 0.00% | G -> A | NA |
LOC_Os02g06640.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g06640.4 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 94.973; most accessible tissue: Zhenshan97 young leaf, score: 99.363 |
| vg0203341433 (J) | chr02 | 3341433 | G | A | 99.30% | 0.00% | G -> A | NA |
LOC_Os02g06640.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g06640.4 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os02g06640.3 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 94.381; most accessible tissue: Zhenshan97 young leaf, score: 99.298 |
| vg0203341480 (J) | chr02 | 3341480 | C | A | 95.20% | 3.77% | C -> A | NA |
LOC_Os02g06640.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g06640.4 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os02g06640.3 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os02g06640.3 Alt: DEL/frameshift_variant(CooVar) LOC_Os02g06640.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os02g06640.4 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 94.452; most accessible tissue: Zhenshan97 young leaf, score: 99.293 |
| vg0203341508 (J) | chr02 | 3341508 | T | Unkown | 96.30% | 3.60% | T -> C | NA |
LOC_Os02g06640.3 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g06640.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os02g06640.4 Alt: DEL/frameshift_variant(CooVar) LOC_Os02g06640.1 Alt: C| synonymous_variant LOW(snpEff) LOC_Os02g06640.4 Alt: C| synonymous_variant LOW(snpEff) LOC_Os02g06640.3 Alt: C| synonymous_variant LOW(snpEff) LOC_Os02g06630.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g06650.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 94.141; most accessible tissue: Zhenshan97 young leaf, score: 99.233 |
| vg0203341517 (J) | chr02 | 3341517 | G | Unkown | 96.40% | 3.58% | G -> A | NA |
LOC_Os02g06640.4 Alt: A| splice_region_variant&intron_variant LOW(snpEff)
LOC_Os02g06640.1 Alt: A| synonymous_variant LOW(snpEff) LOC_Os02g06640.3 Alt: A| synonymous_variant LOW(snpEff) LOC_Os02g06630.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g06650.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g06640.3 Alt: DEL/frameshift_variant(CooVar) LOC_Os02g06640.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 94.124; most accessible tissue: Zhenshan97 young leaf, score: 99.220 |
| vg0203341655 (J) | chr02 | 3341655 | G | A | 99.30% | 0.00% | G -> A | NA |
LOC_Os02g06640.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g06640.3 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 89.531; most accessible tissue: Zhenshan97 young leaf, score: 98.991 |
| vg0203341691 (J) | chr02 | 3341691 | T | C | 93.90% | 0.00% | T -> C | NA |
LOC_Os02g06640.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g06640.3 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 92.906; most accessible tissue: Zhenshan97 young leaf, score: 98.948 |
| vg0203341754 (J) | chr02 | 3341754 | A | G | 95.10% | 0.00% | A -> G | NA |
LOC_Os02g06640.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g06640.3 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 92.872; most accessible tissue: Zhenshan97 young leaf, score: 98.831 |
| vg0203341769 (J) | chr02 | 3341769 | A | T | 98.50% | 1.02% | A -> T | NA |
LOC_Os02g06640.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g06640.3 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os02g06640.3 Alt: DEL/frameshift_variant(CooVar) LOC_Os02g06640.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 92.868; most accessible tissue: Zhenshan97 young leaf, score: 98.794 |
| vg0203341817 (J) | chr02 | 3341817 | A | G | 99.50% | 0.38% | A -> G | NA |
LOC_Os02g06640.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g06640.3 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os02g06640.3 Alt: DEL/frameshift_variant(CooVar) LOC_Os02g06640.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 92.484; most accessible tissue: Zhenshan97 young leaf, score: 98.636 |
| vg0203341968 (J) | chr02 | 3341968 | A | T | 99.60% | 0.00% | A -> T | NA |
LOC_Os02g06640.4 Alt: T| splice_donor_variant&intron_variant HIGH(snpEff)
LOC_Os02g06640.1 Alt: T| missense_variant MODERATE(snpEff) LOC_Os02g06640.3 Alt: T| missense_variant MODERATE(snpEff) LOC_Os02g06630.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 92.395; most accessible tissue: Zhenshan97 young leaf, score: 97.684 |
| vg0203342054 (J) | chr02 | 3342054 | C | A | 94.60% | 0.00% | C -> A | NA |
LOC_Os02g06630.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06650.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g06640.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g06640.4 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g06640.3 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 91.087; most accessible tissue: Zhenshan97 flag leaf, score: 96.910 |
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