23 variations found. LOC_Os06g10300 (OsFBL29 - F-box domain and LRR containing protein; expressed), ranging from 5,295,021 bp to 5,297,673 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0605295186 (J) | chr06 | 5295186 | CGCCGCC GGCGGCC TG | C | 93.00% | 1.67% | CGCCGCCGGC GGCCTG -> C | NA |
LOC_Os06g10300.1 Alt: C| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os06g10300.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 81.086; most accessible tissue: Minghui63 panicle, score: 92.800 |
| vg0605295245 (J) | chr06 | 5295245 | G | T | 98.00% | 0.00% | G -> T | NA |
LOC_Os06g10300.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 76.871; most accessible tissue: Minghui63 panicle, score: 90.624 |
| vg0605295334 (J) | chr06 | 5295334 | G | GGC | 86.90% | 0.00% | G -> GGC | NA |
LOC_Os06g10300.1 Alt: GGC| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 74.165; most accessible tissue: Minghui63 panicle, score: 90.184 |
| vg0605295409 (J) | chr06 | 5295409 | T | G | 86.90% | 0.00% | T -> G,C |
mr1201 (All); LMM P-value: 4.47E-20; LR P-value: 1.56E-38;
mr1201 (Ind_All); LMM P-value: 1.27E-17; LR P-value: 6.65E-38; mr1219 (All); LMM P-value: 8.09E-17; LR P-value: 1.44E-28; mr1219 (Ind_All); LMM P-value: 2.36E-15; LR P-value: 2.26E-33; mr1274 (All); LMM P-value: 1.06E-17; LR P-value: 1.35E-33; mr1274 (Ind_All); LMM P-value: 8.30E-19; LR P-value: 3.34E-34; mr1201_2 (All); LMM P-value: 3.28E-19; LR P-value: 6.68E-35; mr1201_2 (Ind_All); LMM P-value: 2.46E-17; LR P-value: 1.05E-33; mr1219_2 (All); LMM P-value: 6.40E-16; LR P-value: 1.61E-26; mr1219_2 (Ind_All); LMM P-value: 1.27E-15; LR P-value: 5.39E-31; mr1274_2 (All); LMM P-value: 4.62E-14; LR P-value: 2.90E-31; mr1274_2 (Ind_All); LMM P-value: 2.74E-15; LR P-value: 3.17E-32 |
LOC_Os06g10300.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g10300.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 66.492; most accessible tissue: Minghui63 panicle, score: 86.012 |
| vg0605295569 (J) | chr06 | 5295569 | C | A | 87.20% | 0.00% | C -> A |
mr1201 (All); LMM P-value: 2.26E-22; LR P-value: 4.74E-41;
mr1201 (Ind_All); LMM P-value: 2.54E-20; LR P-value: 1.80E-42; mr1219 (All); LMM P-value: 1.30E-18; LR P-value: 1.51E-30; mr1219 (Ind_All); LMM P-value: 9.18E-18; LR P-value: 1.49E-37; mr1274 (All); LMM P-value: 1.06E-20; LR P-value: 2.07E-37; mr1274 (Ind_All); LMM P-value: 2.46E-22; LR P-value: 1.02E-38; mr1201_2 (All); LMM P-value: 6.68E-21; LR P-value: 2.22E-36; mr1201_2 (Ind_All); LMM P-value: 9.50E-20; LR P-value: 6.49E-37; mr1219_2 (All); LMM P-value: 2.08E-17; LR P-value: 6.22E-28; mr1219_2 (Ind_All); LMM P-value: 9.94E-18; LR P-value: 4.34E-34; mr1274_2 (All); LMM P-value: 2.39E-16; LR P-value: 3.02E-34; mr1274_2 (Ind_All); LMM P-value: 3.99E-18; LR P-value: 2.01E-36 |
LOC_Os06g10310.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g10290.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10300.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 53.791; most accessible tissue: Callus, score: 77.043 |
| vg0605295651 (J) | chr06 | 5295651 | A | G | 99.90% | 0.00% | A -> G | NA |
LOC_Os06g10310.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os06g10290.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os06g10300.1 Alt: G| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 46.190; most accessible tissue: Minghui63 panicle, score: 66.554 |
| vg0605295746 (J) | chr06 | 5295746 | C | T | 89.40% | 0.00% | C -> T |
mr1201 (All); LMM P-value: 2.12E-22; LR P-value: 2.59E-40;
mr1201 (Ind_All); LMM P-value: 4.68E-21; LR P-value: 3.67E-43; mr1219 (All); LMM P-value: 1.11E-18; LR P-value: 1.89E-31; mr1219 (Ind_All); LMM P-value: 7.34E-20; LR P-value: 1.75E-39; mr1274 (All); LMM P-value: 1.93E-21; LR P-value: 1.99E-40; mr1274 (Ind_All); LMM P-value: 5.00E-21; LR P-value: 7.17E-38; mr1201_2 (All); LMM P-value: 1.79E-20; LR P-value: 4.76E-37; mr1201_2 (Ind_All); LMM P-value: 1.39E-20; LR P-value: 1.99E-38; mr1219_2 (All); LMM P-value: 4.46E-18; LR P-value: 4.90E-29; mr1219_2 (Ind_All); LMM P-value: 1.18E-19; LR P-value: 4.55E-36; mr1274_2 (All); LMM P-value: 3.82E-19; LR P-value: 8.43E-37; mr1274_2 (Ind_All); LMM P-value: 9.67E-20; LR P-value: 4.39E-38 |
LOC_Os06g10310.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g10290.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10300.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 36.675; most accessible tissue: Callus, score: 76.484 |
| vg0605295840 (J) | chr06 | 5295840 | G | C | 99.90% | 0.00% | G -> C | NA |
LOC_Os06g10310.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
LOC_Os06g10290.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os06g10300.1 Alt: C| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 34.220; most accessible tissue: Callus, score: 54.107 |
| vg0605296103 (J) | chr06 | 5296103 | A | T | 99.80% | 0.00% | A -> T | NA |
LOC_Os06g10300.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os06g10310.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os06g10290.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 38.542; most accessible tissue: Minghui63 panicle, score: 62.157 |
| vg0605296120 (J) | chr06 | 5296120 | C | G | 99.50% | 0.00% | C -> G | NA |
LOC_Os06g10300.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 40.007; most accessible tissue: Minghui63 panicle, score: 64.459 |
| vg0605296250 (J) | chr06 | 5296250 | A | C | 86.90% | 0.00% | A -> C |
mr1201 (All); LMM P-value: 3.97E-23; LR P-value: 5.26E-42;
mr1201 (Ind_All); LMM P-value: 3.10E-21; LR P-value: 1.36E-42; mr1219 (All); LMM P-value: 1.42E-18; LR P-value: 1.20E-30; mr1219 (Ind_All); LMM P-value: 1.25E-17; LR P-value: 9.89E-37; mr1274 (All); LMM P-value: 5.45E-20; LR P-value: 2.11E-36; mr1274 (Ind_All); LMM P-value: 9.00E-22; LR P-value: 4.74E-38; mr1662 (All); LR P-value: 1.62E-06; mr1201_2 (All); LMM P-value: 2.38E-21; LR P-value: 1.76E-37; mr1201_2 (Ind_All); LMM P-value: 8.43E-20; LR P-value: 4.88E-37; mr1219_2 (All); LMM P-value: 2.18E-17; LR P-value: 3.52E-28; mr1219_2 (Ind_All); LMM P-value: 1.52E-17; LR P-value: 1.38E-33; mr1274_2 (All); LMM P-value: 5.72E-16; LR P-value: 5.60E-34; mr1274_2 (Ind_All); LMM P-value: 9.05E-18; LR P-value: 5.78E-36 |
LOC_Os06g10310.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g10290.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10300.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 43.946; most accessible tissue: Callus, score: 68.045 |
| vg0605296290 (J) | chr06 | 5296290 | G | GTTGGT | 86.80% | 0.06% | G -> GTTGGT | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os06g10310.1 Alt: GTTGGT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10290.1 Alt: GTTGGT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10300.1 Alt: GTTGGT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 46.277; most accessible tissue: Minghui63 panicle, score: 70.194 |
| vg0605296292 (J) | chr06 | 5296292 | C | CTGCTG | 86.80% | 0.06% | C -> CTGCTG | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os06g10310.1 Alt: CTGCTG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10290.1 Alt: CTGCTG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10300.1 Alt: CTGCTG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 46.277; most accessible tissue: Minghui63 panicle, score: 70.194 |
| vg0605296565 (J) | chr06 | 5296565 | G | T | 87.10% | 0.02% | G -> T |
mr1201 (All); LMM P-value: 9.96E-23; LR P-value: 5.36E-41;
mr1201 (Ind_All); LMM P-value: 3.10E-21; LR P-value: 1.36E-42; mr1219 (All); LMM P-value: 2.58E-18; LR P-value: 5.30E-30; mr1219 (Ind_All); LMM P-value: 1.25E-17; LR P-value: 9.89E-37; mr1274 (All); LMM P-value: 4.62E-20; LR P-value: 1.09E-36; mr1274 (Ind_All); LMM P-value: 9.00E-22; LR P-value: 4.74E-38; mr1201_2 (All); LMM P-value: 8.22E-21; LR P-value: 2.18E-36; mr1201_2 (Ind_All); LMM P-value: 8.43E-20; LR P-value: 4.88E-37; mr1219_2 (All); LMM P-value: 3.34E-17; LR P-value: 1.32E-27; mr1219_2 (Ind_All); LMM P-value: 1.52E-17; LR P-value: 1.38E-33; mr1274_2 (All); LMM P-value: 6.71E-16; LR P-value: 9.49E-34; mr1274_2 (Ind_All); LMM P-value: 9.05E-18; LR P-value: 5.78E-36 |
LOC_Os06g10300.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g10300.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 50.084; most accessible tissue: Zhenshan97 panicle, score: 79.071 |
| vg0605296614 (J) | chr06 | 5296614 | C | A | 83.10% | 0.00% | C -> A | NA |
LOC_Os06g10300.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 51.860; most accessible tissue: Zhenshan97 panicle, score: 82.336 |
| vg0605296674 (J) | chr06 | 5296674 | T | C | 86.90% | 0.00% | T -> C |
mr1201 (All); LMM P-value: 5.78E-22; LR P-value: 6.19E-44;
mr1201 (Ind_All); LMM P-value: 5.77E-25; LR P-value: 6.35E-47; mr1219 (All); LMM P-value: 2.61E-19; LR P-value: 1.41E-32; mr1219 (Ind_All); LMM P-value: 1.85E-21; LR P-value: 2.40E-41; mr1274 (All); LMM P-value: 9.89E-20; LR P-value: 2.71E-37; mr1274 (Ind_All); LMM P-value: 5.89E-25; LR P-value: 5.24E-41; mr1201_2 (All); LMM P-value: 9.57E-23; LR P-value: 2.41E-40; mr1201_2 (Ind_All); LMM P-value: 1.73E-23; LR P-value: 2.91E-41; mr1219_2 (All); LMM P-value: 1.88E-18; LR P-value: 2.79E-30; mr1219_2 (Ind_All); LMM P-value: 1.03E-21; LR P-value: 2.64E-38; mr1274_2 (All); LMM P-value: 1.48E-16; LR P-value: 2.73E-36; mr1274_2 (Ind_All); LMM P-value: 1.69E-21; LR P-value: 2.40E-40 |
LOC_Os06g10300.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 51.572; most accessible tissue: Zhenshan97 panicle, score: 82.888 |
| vg0605296817 (J) | chr06 | 5296817 | A | T | 87.10% | 0.13% | A -> T |
mr1201 (All); LMM P-value: 8.11E-21; LR P-value: 6.15E-40;
mr1201 (Ind_All); LMM P-value: 3.53E-18; LR P-value: 1.26E-39; mr1219 (All); LMM P-value: 1.35E-17; LR P-value: 9.92E-30; mr1219 (Ind_All); LMM P-value: 3.19E-16; LR P-value: 4.66E-35; mr1274 (All); LMM P-value: 8.83E-19; LR P-value: 4.83E-35; mr1274 (Ind_All); LMM P-value: 5.84E-20; LR P-value: 3.82E-36; mr1201_2 (All); LMM P-value: 1.29E-19; LR P-value: 1.31E-35; mr1201_2 (Ind_All); LMM P-value: 1.17E-17; LR P-value: 1.65E-34; mr1219_2 (All); LMM P-value: 2.07E-16; LR P-value: 3.13E-27; mr1219_2 (Ind_All); LMM P-value: 3.80E-16; LR P-value: 6.20E-32; mr1274_2 (All); LMM P-value: 5.30E-15; LR P-value: 1.26E-32; mr1274_2 (Ind_All); LMM P-value: 2.22E-16; LR P-value: 5.27E-34 |
LOC_Os06g10300.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g10300.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 46.285; most accessible tissue: Zhenshan97 panicle, score: 74.671 |
| vg0605296935 (J) | chr06 | 5296935 | GT | GTT | 87.00% | 0.00% | GT -> GTT,G,GTTT | NA |
LOC_Os06g10310.1 Alt: GTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g10290.1 Alt: GTTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10300.1 Alt: GTTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10310.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10290.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10300.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10310.1 Alt: GTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10290.1 Alt: GTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g10300.1 Alt: GTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 49.895; most accessible tissue: Minghui63 panicle, score: 77.956 |
| vg0605296993 (J) | chr06 | 5296993 | A | T | 99.90% | 0.00% | A -> T | NA |
LOC_Os06g10300.1 Alt: T| stop_gained HIGH(snpEff)
LOC_Os06g10310.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 49.813; most accessible tissue: Zhenshan97 panicle, score: 77.482 |
| vg0605297089 (J) | chr06 | 5297089 | T | C | 89.30% | 0.00% | T -> C |
mr1201 (All); LMM P-value: 5.37E-23; LR P-value: 3.83E-41;
mr1201 (Ind_All); LMM P-value: 1.16E-21; LR P-value: 2.88E-44; mr1219 (All); LMM P-value: 1.60E-18; LR P-value: 1.67E-31; mr1219 (Ind_All); LMM P-value: 4.50E-19; LR P-value: 1.43E-39; mr1274 (All); LMM P-value: 1.63E-22; LR P-value: 5.20E-42; mr1274 (Ind_All); LMM P-value: 2.29E-22; LR P-value: 1.08E-39; mr1201_2 (All); LMM P-value: 7.65E-21; LR P-value: 2.41E-37; mr1201_2 (Ind_All); LMM P-value: 5.12E-21; LR P-value: 8.39E-39; mr1219_2 (All); LMM P-value: 1.94E-17; LR P-value: 1.27E-28; mr1219_2 (Ind_All); LMM P-value: 1.36E-18; LR P-value: 2.00E-35; mr1274_2 (All); LMM P-value: 7.37E-19; LR P-value: 5.84E-37; mr1274_2 (Ind_All); LMM P-value: 2.02E-19; LR P-value: 2.76E-38 |
LOC_Os06g10300.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 44.819; most accessible tissue: Zhenshan97 panicle, score: 75.670 |
| vg0605297560 (J) | chr06 | 5297560 | G | C | 99.40% | 0.00% | G -> C | NA |
LOC_Os06g10300.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 78.570; most accessible tissue: Minghui63 panicle, score: 95.218 |
| vg0605297587 (J) | chr06 | 5297587 | A | C | 99.90% | 0.00% | A -> C | NA |
LOC_Os06g10300.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os06g10310.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os06g10290.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 78.516; most accessible tissue: Minghui63 panicle, score: 95.468 |
| STR0605296673 (J) | chr06 | 5296673 | CT | CC | 88.20% | 0.00% | CT -> CC | NA |
|