29 variations found. LOC_Os02g04510 (UOS1; putative; expressed), ranging from 2,001,886 bp to 2,005,972 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0202001992 (J) | chr02 | 2001992 | A | G | 96.70% | 0.00% | A -> G | NA |
LOC_Os02g04510.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 98.076; most accessible tissue: Zhenshan97 flag leaf, score: 99.514 |
| vg0202002417 (J) | chr02 | 2002417 | C | T | 99.40% | 0.00% | C -> T | NA |
LOC_Os02g04510.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 85.792; most accessible tissue: Minghui63 flag leaf, score: 96.850 |
| vg0202002464 (J) | chr02 | 2002464 | G | T | 97.20% | 0.00% | G -> T | NA |
LOC_Os02g04510.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 86.053; most accessible tissue: Minghui63 flag leaf, score: 95.880 |
| vg0202002569 (J) | chr02 | 2002569 | T | A | 97.20% | 0.00% | T -> A | NA |
LOC_Os02g04520.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g04520.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04510.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 82.733; most accessible tissue: Minghui63 flag leaf, score: 94.110 |
| vg0202002667 (J) | chr02 | 2002667 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os02g04520.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os02g04520.2 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g04500.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g04500.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g04510.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 73.816; most accessible tissue: Minghui63 flag leaf, score: 89.997 |
| vg0202002675 (J) | chr02 | 2002675 | C | A | 97.20% | 0.00% | C -> A | NA |
LOC_Os02g04520.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g04520.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04510.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.996; most accessible tissue: Minghui63 flag leaf, score: 89.718 |
| vg0202002728 (J) | chr02 | 2002728 | G | A | 96.70% | 0.00% | G -> A | NA |
LOC_Os02g04520.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g04520.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04510.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 73.534; most accessible tissue: Minghui63 flag leaf, score: 87.189 |
| vg0202002748 (J) | chr02 | 2002748 | G | A | 96.80% | 0.00% | G -> A | NA |
LOC_Os02g04520.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g04520.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04510.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 73.118; most accessible tissue: Minghui63 flag leaf, score: 88.103 |
| vg0202002759 (J) | chr02 | 2002759 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os02g04520.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g04520.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04510.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 73.266; most accessible tissue: Minghui63 flag leaf, score: 88.459 |
| vg0202002803 (J) | chr02 | 2002803 | AT | A | 95.70% | 0.00% | AT -> A,ATTT,ATT ,TT | NA |
LOC_Os02g04520.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g04520.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04510.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04520.1 Alt: ATT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04520.2 Alt: ATT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.1 Alt: ATT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.2 Alt: ATT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04510.1 Alt: ATT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04520.1 Alt: TT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04520.2 Alt: TT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.1 Alt: TT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.2 Alt: TT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04510.1 Alt: TT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04520.1 Alt: ATTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04520.2 Alt: ATTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.1 Alt: ATTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.2 Alt: ATTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04510.1 Alt: ATTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 71.693; most accessible tissue: Minghui63 flag leaf, score: 88.574 |
| vg0202002931 (J) | chr02 | 2002931 | C | T | 96.70% | 0.00% | C -> T | NA |
LOC_Os02g04510.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 63.425; most accessible tissue: Minghui63 flag leaf, score: 83.412 |
| vg0202003459 (J) | chr02 | 2003459 | C | A | 99.70% | 0.00% | C -> A | NA |
LOC_Os02g04520.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g04520.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04510.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 58.986; most accessible tissue: Minghui63 flag leaf, score: 74.955 |
| vg0202003809 (J) | chr02 | 2003809 | C | T | 99.70% | 0.00% | C -> T | NA |
LOC_Os02g04520.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g04520.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04510.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 70.262; most accessible tissue: Minghui63 flag leaf, score: 88.687 |
| vg0202003824 (J) | chr02 | 2003824 | C | A | 96.70% | 0.00% | C -> A | NA |
LOC_Os02g04520.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g04520.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04510.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 70.785; most accessible tissue: Minghui63 flag leaf, score: 89.016 |
| vg0202004000 (J) | chr02 | 2004000 | C | A | 96.60% | 0.00% | C -> A,CA | NA |
LOC_Os02g04510.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g04510.1 Alt: CA| frameshift_variant&splice_region_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 66.659; most accessible tissue: Minghui63 flag leaf, score: 86.911 |
| vg0202004329 (J) | chr02 | 2004329 | A | G | 96.80% | 0.00% | A -> G | NA |
LOC_Os02g04510.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 54.936; most accessible tissue: Minghui63 flag leaf, score: 84.227 |
| vg0202004508 (J) | chr02 | 2004508 | TACA | T | 99.80% | 0.00% | TACA -> T | NA |
LOC_Os02g04510.1 Alt: T| splice_region_variant&intron_variant LOW(snpEff)
LOC_Os02g04520.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g04520.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g04500.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g04500.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 61.964; most accessible tissue: Minghui63 flag leaf, score: 88.103 |
| vg0202004534 (J) | chr02 | 2004534 | C | CT | 96.70% | 0.00% | C -> CT | NA |
LOC_Os02g04520.1 Alt: CT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g04520.2 Alt: CT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.1 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.2 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04510.1 Alt: CT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 60.289; most accessible tissue: Minghui63 flag leaf, score: 87.461 |
| vg0202005079 (J) | chr02 | 2005079 | GA | G | 96.40% | 0.00% | GA -> G,GAA | NA |
LOC_Os02g04510.1 Alt: G| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os02g04520.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04520.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04510.1 Alt: GAA| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os02g04520.1 Alt: GAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04520.2 Alt: GAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.1 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.2 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 72.285; most accessible tissue: Minghui63 flag leaf, score: 93.326 |
| vg0202005082 (J) | chr02 | 2005082 | A | G | 99.70% | 0.00% | A -> G | NA |
LOC_Os02g04520.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g04520.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04510.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 71.925; most accessible tissue: Minghui63 flag leaf, score: 93.280 |
| vg0202005149 (J) | chr02 | 2005149 | A | C | 98.20% | 0.00% | A -> C |
LOC_Os02g04520.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g04520.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04510.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 71.254; most accessible tissue: Minghui63 flag leaf, score: 93.673 |
|
| vg0202005259 (J) | chr02 | 2005259 | A | G | 96.80% | 0.00% | A -> G | NA |
LOC_Os02g04520.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g04520.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04510.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 71.616; most accessible tissue: Minghui63 flag leaf, score: 93.996 |
| vg0202005284 (J) | chr02 | 2005284 | G | A | 96.70% | 0.00% | G -> A | NA |
LOC_Os02g04520.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g04520.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04510.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 74.884; most accessible tissue: Minghui63 flag leaf, score: 94.880 |
| vg0202005341 (J) | chr02 | 2005341 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os02g04510.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os02g04520.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g04520.2 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g04500.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g04500.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 75.523; most accessible tissue: Minghui63 flag leaf, score: 95.751 |
| vg0202005353 (J) | chr02 | 2005353 | G | A | 96.80% | 0.00% | G -> A | NA |
LOC_Os02g04510.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 76.146; most accessible tissue: Minghui63 flag leaf, score: 95.569 |
| vg0202005637 (J) | chr02 | 2005637 | G | T | 96.80% | 0.00% | G -> T | NA |
LOC_Os02g04510.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g04520.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04520.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 78.899; most accessible tissue: Minghui63 flag leaf, score: 96.674 |
| vg0202005678 (J) | chr02 | 2005678 | G | A | 99.40% | 0.00% | G -> A | NA |
LOC_Os02g04510.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os02g04520.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g04520.2 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g04500.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g04500.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 78.540; most accessible tissue: Minghui63 flag leaf, score: 96.400 |
| vg0202005726 (J) | chr02 | 2005726 | A | G | 96.70% | 0.00% | A -> G | NA |
LOC_Os02g04510.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g04520.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04520.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.744; most accessible tissue: Minghui63 flag leaf, score: 95.838 |
| vg0202005758 (J) | chr02 | 2005758 | G | A | 96.80% | 0.00% | G -> A | NA |
LOC_Os02g04510.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g04520.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04520.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g04500.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 73.283; most accessible tissue: Minghui63 flag leaf, score: 95.545 |