6 variations found. Os01g0213100/LOC_Os01g11490 (zinc finger; C3HC4 type domain containing protein; expressed), ranging from 6,185,621 bp to 6,186,317 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os01g11490 | zinc finger, C3HC4 type domain containing protein; RAP ID: Os01g0213100; MSU ID: LOC_Os01g11490 |
The expression data is from the CREP database. And the expression value is log2-transformed. Move the mouse over the cells of the heat map to get detailed tissue information and expression values.
| 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0106185629 (J) | chr01 | 6185629 | G | T | 71.50% | 0.00% | G -> T |
mr1002 (All); LR P-value: 6.11E-08;
mr1207 (All); LR P-value: 1.69E-10; mr1345 (All); LR P-value: 5.36E-06; mr1498 (Ind_All); LMM P-value: 1.65E-08; LR P-value: 4.36E-10; mr1756 (All); LR P-value: 1.06E-07; mr1769 (All); LMM P-value: 2.89E-07; LR P-value: 1.18E-12; mr1769 (Ind_All); LMM P-value: 1.59E-07; LR P-value: 1.72E-12; mr1925 (Ind_All); LR P-value: 2.57E-06; mr1943 (Ind_All); LR P-value: 9.21E-06; mr1951 (All); LMM P-value: 2.42E-06; mr1951 (Ind_All); LMM P-value: 3.22E-08; LR P-value: 2.07E-07; mr1063_2 (Jap_All); LR P-value: 4.00E-06; mr1180_2 (Jap_All); LR P-value: 2.29E-08; mr1183_2 (Jap_All); LR P-value: 4.53E-08; mr1236_2 (All); LR P-value: 4.42E-06; mr1295_2 (All); LR P-value: 2.99E-06; mr1310_2 (Ind_All); LMM P-value: 4.78E-06; LR P-value: 3.43E-11; mr1405_2 (All); LR P-value: 6.61E-06; mr1498_2 (All); LMM P-value: 1.40E-06; LR P-value: 1.65E-08; mr1498_2 (Ind_All); LR P-value: 3.15E-09; mr1769_2 (All); LMM P-value: 3.43E-09; LR P-value: 2.32E-21; mr1769_2 (Ind_All); LMM P-value: 4.56E-07; LR P-value: 4.43E-15; mr1769_2 (Jap_All); LR P-value: 1.39E-13; mr1794_2 (Jap_All); LR P-value: 3.90E-08; mr1808_2 (All); LR P-value: 5.35E-07; mr1829_2 (All); LR P-value: 1.20E-08; mr1943_2 (Ind_All); LR P-value: 5.87E-09; mr1951_2 (Ind_All); LR P-value: 1.77E-06 |
LOC_Os01g11490.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 76.494; most accessible tissue: Zhenshan97 flower, score: 88.021 |
| vg0106185784 (J) | chr01 | 6185784 | G | A | 86.90% | 0.00% | G -> A | NA |
LOC_Os01g11490.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 84.068; most accessible tissue: Zhenshan97 flower, score: 89.639 |
| vg0106185961 (J) | chr01 | 6185961 | G | A | 98.70% | 0.00% | G -> A | NA |
LOC_Os01g11490.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 83.514; most accessible tissue: Zhenshan97 panicle, score: 90.268 |
| vg0106186003 (J) | chr01 | 6186003 | GGCCGCC GCCGCC | GGCCGCC GCC | 64.40% | 0.00% | GGCCGCCGCC GCC -> GGCCGCCGCC ,G,GGCC | NA |
LOC_Os01g11490.1 Alt: G| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os01g11490.1 Alt: GGCCGCCGCC| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar) LOC_Os01g11490.1 Alt: GGCC| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 82.179; most accessible tissue: Zhenshan97 panicle, score: 89.389 |
| vg0106186026 (J) | chr01 | 6186026 | C | A | 64.30% | 0.02% | C -> A | NA |
LOC_Os01g11490.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g11490.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 82.435; most accessible tissue: Zhenshan97 panicle, score: 89.389 |
| vg0106186306 (J) | chr01 | 6186306 | G | A | 77.90% | 0.00% | A -> G |
mr1368 (All); LR P-value: 2.88E-10;
mr1368 (Jap_All); LR P-value: 4.78E-06; mr1584 (All); LR P-value: 1.80E-21; mr1129_2 (Jap_All); LR P-value: 7.81E-06; mr1180_2 (Jap_All); LR P-value: 1.82E-07; mr1183_2 (Jap_All); LR P-value: 1.29E-06; mr1251_2 (Jap_All); LR P-value: 1.68E-08; mr1435_2 (Jap_All); LR P-value: 1.78E-08; mr1769_2 (All); LR P-value: 2.79E-10; mr1769_2 (Jap_All); LR P-value: 6.50E-13; mr1771_2 (All); LR P-value: 2.97E-41; mr1785_2 (All); LR P-value: 2.52E-06; mr1794_2 (Jap_All); LR P-value: 3.87E-08; mr1800_2 (All); LR P-value: 8.74E-14; mr1840_2 (All); LR P-value: 9.56E-07; mr1844_2 (All); LR P-value: 5.96E-11; mr1952_2 (All); LR P-value: 6.84E-07 |
LOC_Os01g11490.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 85.628; most accessible tissue: Zhenshan97 flower, score: 92.841 |