10 variations found. LOC_Os05g36360 (U-box domain containing protein; expressed), ranging from 21,525,164 bp to 21,526,787 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0521525472 (J) | chr05 | 21525472 | A | C | 62.90% | 0.89% | C -> A |
mr1027 (All); LR P-value: 1.63E-71;
mr1218 (All); LR P-value: 7.05E-14; mr1517 (All); LR P-value: 6.42E-88; mr1542 (All); LR P-value: 5.91E-37; mr1595 (All); LR P-value: 2.72E-08; mr1672 (All); LR P-value: 4.11E-82; mr1718 (All); LR P-value: 2.33E-80; mr1758 (All); LR P-value: 8.53E-88; mr1795 (All); LR P-value: 8.80E-54; mr1888 (All); LR P-value: 1.38E-22; mr1890 (All); LR P-value: 2.33E-38; mr1962 (All); LR P-value: 4.78E-60; mr1064_2 (All); LR P-value: 6.05E-58; mr1087_2 (All); LR P-value: 3.43E-71; mr1124_2 (All); LR P-value: 4.76E-54; mr1536_2 (All); LR P-value: 3.09E-94; mr1595_2 (All); LR P-value: 5.16E-10; mr1609_2 (All); LR P-value: 5.23E-22; mr1689_2 (All); LR P-value: 1.72E-38; mr1718_2 (All); LR P-value: 4.95E-108; mr1795_2 (All); LR P-value: 1.50E-89; mr1888_2 (All); LR P-value: 4.16E-39 |
LOC_Os05g36360.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g36360.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 97.525; most accessible tissue: Zhenshan97 flag leaf, score: 99.334 |
| vg0521525775 (J) | chr05 | 21525775 | G | A | 60.10% | 0.00% | G -> A | NA |
LOC_Os05g36360.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 94.336; most accessible tissue: Zhenshan97 flag leaf, score: 98.188 |
| vg0521526344 (J) | chr05 | 21526344 | G | T | 63.80% | 0.00% | T -> G | NA |
LOC_Os05g36360.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 93.532; most accessible tissue: Zhenshan97 flag leaf, score: 97.840 |
| vg0521526398 (J) | chr05 | 21526398 | G | A | 98.30% | 0.00% | G -> A | NA |
LOC_Os05g36360.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 93.682; most accessible tissue: Zhenshan97 flag leaf, score: 97.871 |
| vg0521526540 (J) | chr05 | 21526540 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os05g36360.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os05g36370.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os05g36380.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 94.508; most accessible tissue: Zhenshan97 flag leaf, score: 96.918 |
| vg0521526593 (J) | chr05 | 21526593 | T | C | 63.50% | 0.00% | C -> T |
mr1027 (All); LR P-value: 2.32E-71;
mr1218 (All); LR P-value: 3.20E-14; mr1517 (All); LR P-value: 1.53E-86; mr1542 (All); LR P-value: 1.44E-36; mr1718 (All); LR P-value: 1.28E-79; mr1795 (All); LR P-value: 5.12E-54; mr1890 (All); LR P-value: 2.35E-38; mr1962 (All); LR P-value: 1.74E-58; mr1064_2 (All); LR P-value: 1.18E-58; mr1087_2 (All); LR P-value: 3.51E-71; mr1181_2 (All); LR P-value: 2.98E-34; mr1484_2 (All); LR P-value: 1.04E-24; mr1536_2 (All); LR P-value: 2.85E-94; mr1609_2 (All); LR P-value: 1.05E-22; mr1689_2 (All); LR P-value: 9.69E-37; mr1718_2 (All); LR P-value: 7.33E-107; mr1795_2 (All); LR P-value: 2.19E-87; mr1841_2 (All); LR P-value: 3.59E-32; mr1888_2 (All); LR P-value: 1.69E-38; mr1945_2 (All); LR P-value: 2.33E-18 |
LOC_Os05g36360.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g36370.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g36380.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 92.995; most accessible tissue: Zhenshan97 flag leaf, score: 96.316 |
| vg0521526638 (J) | chr05 | 21526638 | G | GA | 63.90% | 0.00% | GA -> G | NA |
LOC_Os05g36360.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g36370.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g36380.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 92.385; most accessible tissue: Zhenshan97 flag leaf, score: 96.182 |
| vg0521526735 (J) | chr05 | 21526735 | G | GA | 97.20% | 0.49% | G -> GA | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g36360.1 Alt: GA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g36370.1 Alt: GA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g36380.1 Alt: GA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 90.146; most accessible tissue: Callus, score: 96.649 |
| vg0521526746 (J) | chr05 | 21526746 | C | CT | 60.10% | 0.02% | C -> CT | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g36360.1 Alt: CT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g36370.1 Alt: CT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g36380.1 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 89.841; most accessible tissue: Callus, score: 96.649 |
| STR0521526639 (J) | chr05 | 21526639 | AA | AAA | 63.30% | 0.00% | AAA -> AA | NA |
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