12 variations found. LOC_Os02g47770 (ZF-HD protein dimerisation region containing protein; expressed), ranging from 29,206,031 bp to 29,208,132 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0229206055 (J) | chr02 | 29206055 | GC | G | 95.10% | 0.00% | GC -> G | NA |
LOC_Os02g47770.1 Alt: G| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 85.328; most accessible tissue: Zhenshan97 panicle, score: 99.254 |
| vg0229206270 (J) | chr02 | 29206270 | C | T | 96.30% | 0.00% | C -> T | NA |
LOC_Os02g47760.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g47770.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 88.152; most accessible tissue: Zhenshan97 panicle, score: 99.467 |
| vg0229206399 (J) | chr02 | 29206399 | TG | T | 59.30% | 0.00% | TG -> T | NA |
LOC_Os02g47760.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g47770.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 87.795; most accessible tissue: Zhenshan97 panicle, score: 99.425 |
| vg0229206428 (J) | chr02 | 29206428 | G | C | 59.40% | 0.00% | G -> C |
mr1069 (All); LR P-value: 2.22E-12;
mr1069 (Ind_All); LR P-value: 5.21E-08; mr1072 (Ind_All); LR P-value: 2.27E-06; mr1077 (All); LR P-value: 1.73E-20; mr1077 (Ind_All); LR P-value: 8.33E-07; mr1100 (Ind_All); LR P-value: 6.93E-06; mr1124 (Ind_All); LR P-value: 5.79E-06; mr1592 (All); LR P-value: 8.51E-17; mr1592 (Ind_All); LR P-value: 1.66E-06; mr1827 (All); LR P-value: 3.29E-09; mr1842 (Ind_All); LR P-value: 6.88E-06; mr1861 (Ind_All); LR P-value: 2.08E-08; mr1962 (Ind_All); LR P-value: 3.87E-08; mr1124_2 (Ind_All); LR P-value: 2.87E-08; mr1148_2 (All); LR P-value: 6.26E-15; mr1150_2 (Ind_All); LR P-value: 4.08E-06; mr1531_2 (All); LR P-value: 1.48E-22; mr1531_2 (Ind_All); LR P-value: 4.57E-09; mr1861_2 (Ind_All); LR P-value: 3.92E-09 |
LOC_Os02g47760.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g47770.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 87.865; most accessible tissue: Zhenshan97 panicle, score: 99.363 |
| vg0229206897 (J) | chr02 | 29206897 | GTGGTGG TGA | G | 97.80% | 0.00% | GTGGTGGTGA -> G | NA |
LOC_Os02g47760.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g47770.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 82.522; most accessible tissue: Zhenshan97 panicle, score: 96.894 |
| vg0229206925 (J) | chr02 | 29206925 | TGAG | T | 99.90% | 0.00% | TGAG -> T | NA |
LOC_Os02g47760.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os02g47770.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 85.270; most accessible tissue: Zhenshan97 panicle, score: 97.147 |
| vg0229206992 (J) | chr02 | 29206992 | G | A | 84.60% | 0.00% | G -> A |
mr1069 (Ind_All); LR P-value: 4.09E-07;
mr1077 (Ind_All); LR P-value: 4.94E-07; mr1100 (Ind_All); LR P-value: 5.20E-06; mr1798 (Ind_All); LR P-value: 2.60E-06; mr1861 (Ind_All); LR P-value: 5.22E-07; mr1962 (Ind_All); LR P-value: 1.17E-07; mr1124_2 (Ind_All); LR P-value: 3.98E-08; mr1861_2 (Ind_All); LR P-value: 6.82E-09 |
LOC_Os02g47760.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g47770.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 86.576; most accessible tissue: Zhenshan97 panicle, score: 96.832 |
| vg0229207794 (J) | chr02 | 29207794 | C | A | 56.20% | 0.00% | A -> C |
mr1083 (All); LR P-value: 5.67E-23;
mr1088 (All); LR P-value: 6.04E-58; mr1208 (All); LR P-value: 6.05E-30; mr1233 (All); LR P-value: 1.50E-11; mr1246 (All); LR P-value: 1.20E-62; mr1655 (All); LR P-value: 1.04E-12; mr1721 (All); LR P-value: 1.07E-42; mr1916 (All); LR P-value: 3.70E-15; mr1039_2 (All); LR P-value: 1.11E-28; mr1151_2 (All); LR P-value: 4.40E-12; mr1164_2 (All); LR P-value: 5.60E-21; mr1514_2 (All); LR P-value: 1.67E-14; mr1531_2 (All); LR P-value: 8.52E-20 |
LOC_Os02g47770.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 89.452; most accessible tissue: Zhenshan97 panicle, score: 96.982 |
| vg0229207890 (J) | chr02 | 29207890 | C | G | 94.40% | 0.00% | C -> G | NA |
LOC_Os02g47770.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 87.456; most accessible tissue: Zhenshan97 panicle, score: 96.528 |
| vg0229208015 (J) | chr02 | 29208015 | G | GCGCCGC | 84.90% | 0.00% | G -> GCGCCGC,GC GCCGCCGC | NA |
LOC_Os02g47770.1 Alt: GCGCCGCCGC| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os02g47770.1 Alt: GCGCCGC| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 90.996; most accessible tissue: Zhenshan97 panicle, score: 96.668 |
| vg0229208023 (J) | chr02 | 29208023 | G | A | 82.10% | 0.00% | G -> A | NA |
LOC_Os02g47770.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 91.036; most accessible tissue: Zhenshan97 panicle, score: 96.634 |
| STR0229206062 (J) | chr02 | 29206062 | AA | A | 96.60% | 0.00% | AA -> A | NA |
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