11 variations found. LOC_Os03g50900 (transposon protein; putative; unclassified; expressed), ranging from 29,076,705 bp to 29,079,305 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0329077241 (J) | chr03 | 29077241 | T | A | 86.20% | 0.00% | T -> A |
mr1054 (All); LR P-value: 6.69E-06;
mr1073 (All); LR P-value: 9.11E-10; mr1098 (All); LR P-value: 2.80E-32; mr1099 (All); LR P-value: 4.96E-31; mr1101 (All); LR P-value: 8.51E-29; mr1113 (All); LR P-value: 1.24E-15; mr1117 (All); LR P-value: 6.35E-21; mr1119 (All); LR P-value: 8.39E-19; mr1120 (All); LR P-value: 1.59E-26; mr1123 (All); LR P-value: 1.31E-25; mr1146 (All); LR P-value: 1.90E-14; mr1153 (All); LR P-value: 4.38E-06; mr1166 (All); LR P-value: 5.36E-15; mr1184 (All); LR P-value: 1.21E-06; mr1232 (All); LR P-value: 4.99E-10; mr1247 (All); LR P-value: 2.14E-22; mr1283 (All); LR P-value: 2.30E-06; mr1286 (All); LR P-value: 3.37E-06; mr1287 (All); LR P-value: 8.37E-06; mr1307 (All); LR P-value: 3.12E-10; mr1312 (All); LR P-value: 7.82E-07; mr1320 (All); LR P-value: 7.82E-08; mr1348 (All); LR P-value: 3.71E-08; mr1365 (All); LR P-value: 1.48E-06; mr1369 (All); LR P-value: 6.60E-07; mr1373 (All); LR P-value: 5.02E-06; mr1382 (All); LR P-value: 6.22E-07; mr1393 (All); LR P-value: 1.66E-06; mr1409 (All); LR P-value: 8.75E-12; mr1417 (All); LR P-value: 6.82E-07; mr1424 (All); LR P-value: 9.04E-06; mr1438 (All); LR P-value: 4.32E-06; mr1442 (All); LR P-value: 1.20E-09; mr1453 (All); LR P-value: 4.11E-07; mr1474 (All); LR P-value: 2.79E-06; mr1475 (All); LR P-value: 2.79E-06; mr1496 (All); LR P-value: 3.66E-15; mr1512 (All); LR P-value: 1.78E-06; mr1523 (All); LR P-value: 1.38E-06; mr1545 (All); LR P-value: 5.72E-07; mr1574 (All); LR P-value: 4.08E-06; mr1589 (All); LR P-value: 4.43E-24; mr1612 (All); LR P-value: 5.79E-11; mr1633 (All); LR P-value: 1.63E-06; mr1665 (All); LR P-value: 4.30E-06; mr1696 (All); LR P-value: 9.19E-11; mr1706 (All); LR P-value: 1.30E-07; mr1730 (All); LR P-value: 2.96E-11; mr1762 (All); LR P-value: 4.54E-08; mr1774 (All); LR P-value: 1.97E-06; mr1777 (All); LR P-value: 2.49E-07; mr1858 (All); LR P-value: 2.81E-27; mr1859 (All); LR P-value: 2.56E-27; mr1866 (All); LR P-value: 1.06E-10; mr1868 (All); LR P-value: 2.25E-27; mr1917 (All); LR P-value: 1.86E-23; mr1918 (All); LR P-value: 4.29E-13; mr1939 (All); LR P-value: 1.02E-08; mr1961 (All); LR P-value: 6.26E-19; mr1740_2 (All); LR P-value: 1.44E-06; mr1741_2 (All); LR P-value: 1.43E-09 |
LOC_Os03g50900.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 82.093; most accessible tissue: Callus, score: 94.983 |
| vg0329077705 (J) | chr03 | 29077705 | A | C | 86.30% | 0.00% | A -> C |
mr1054 (All); LR P-value: 6.69E-06;
mr1073 (All); LR P-value: 9.11E-10; mr1098 (All); LR P-value: 2.80E-32; mr1099 (All); LR P-value: 4.96E-31; mr1101 (All); LR P-value: 8.51E-29; mr1113 (All); LR P-value: 1.24E-15; mr1117 (All); LR P-value: 6.35E-21; mr1119 (All); LR P-value: 8.39E-19; mr1120 (All); LR P-value: 1.59E-26; mr1123 (All); LR P-value: 1.31E-25; mr1146 (All); LR P-value: 1.90E-14; mr1153 (All); LR P-value: 4.38E-06; mr1166 (All); LR P-value: 5.36E-15; mr1184 (All); LR P-value: 1.21E-06; mr1232 (All); LR P-value: 4.99E-10; mr1247 (All); LR P-value: 2.14E-22; mr1283 (All); LR P-value: 2.30E-06; mr1286 (All); LR P-value: 3.37E-06; mr1287 (All); LR P-value: 8.37E-06; mr1307 (All); LR P-value: 3.12E-10; mr1312 (All); LR P-value: 7.82E-07; mr1320 (All); LR P-value: 7.82E-08; mr1348 (All); LR P-value: 3.71E-08; mr1365 (All); LR P-value: 1.48E-06; mr1369 (All); LR P-value: 6.60E-07; mr1373 (All); LR P-value: 5.02E-06; mr1382 (All); LR P-value: 6.22E-07; mr1393 (All); LR P-value: 1.66E-06; mr1409 (All); LR P-value: 8.75E-12; mr1417 (All); LR P-value: 6.82E-07; mr1424 (All); LR P-value: 9.04E-06; mr1438 (All); LR P-value: 4.32E-06; mr1442 (All); LR P-value: 1.20E-09; mr1453 (All); LR P-value: 4.11E-07; mr1474 (All); LR P-value: 2.79E-06; mr1475 (All); LR P-value: 2.79E-06; mr1496 (All); LR P-value: 3.66E-15; mr1512 (All); LR P-value: 1.78E-06; mr1523 (All); LR P-value: 1.38E-06; mr1545 (All); LR P-value: 5.72E-07; mr1574 (All); LR P-value: 4.08E-06; mr1589 (All); LR P-value: 4.43E-24; mr1612 (All); LR P-value: 5.79E-11; mr1633 (All); LR P-value: 1.63E-06; mr1665 (All); LR P-value: 4.30E-06; mr1696 (All); LR P-value: 9.19E-11; mr1706 (All); LR P-value: 1.30E-07; mr1730 (All); LR P-value: 2.96E-11; mr1762 (All); LR P-value: 4.54E-08; mr1774 (All); LR P-value: 1.97E-06; mr1777 (All); LR P-value: 2.49E-07; mr1858 (All); LR P-value: 2.81E-27; mr1859 (All); LR P-value: 2.56E-27; mr1866 (All); LR P-value: 1.06E-10; mr1868 (All); LR P-value: 2.25E-27; mr1917 (All); LR P-value: 1.86E-23; mr1918 (All); LR P-value: 4.29E-13; mr1939 (All); LR P-value: 1.02E-08; mr1961 (All); LR P-value: 6.26E-19; mr1740_2 (All); LR P-value: 1.44E-06; mr1741_2 (All); LR P-value: 1.43E-09 |
LOC_Os03g50900.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 65.911; most accessible tissue: Callus, score: 85.132 |
| vg0329078075 (J) | chr03 | 29078075 | A | G | 99.30% | 0.00% | A -> G | NA |
LOC_Os03g50900.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os03g50885.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 47.381; most accessible tissue: Callus, score: 86.625 |
| vg0329078090 (J) | chr03 | 29078090 | T | C | 86.30% | 0.00% | T -> C |
mr1073 (All); LR P-value: 6.80E-08;
mr1098 (All); LR P-value: 1.07E-29; mr1099 (All); LR P-value: 6.51E-30; mr1101 (All); LR P-value: 2.22E-27; mr1113 (All); LR P-value: 3.76E-16; mr1114 (All); LR P-value: 1.03E-17; mr1116 (All); LR P-value: 3.31E-17; mr1117 (All); LR P-value: 1.08E-21; mr1119 (All); LR P-value: 1.76E-18; mr1120 (All); LR P-value: 5.44E-27; mr1123 (All); LR P-value: 3.56E-25; mr1166 (All); LR P-value: 2.15E-14; mr1184 (All); LR P-value: 4.84E-06; mr1247 (All); LR P-value: 1.08E-21; mr1312 (All); LR P-value: 3.53E-06; mr1320 (All); LR P-value: 7.89E-07; mr1369 (All); LR P-value: 2.63E-07; mr1373 (All); LR P-value: 1.17E-06; mr1382 (All); LR P-value: 1.40E-06; mr1393 (All); LR P-value: 5.01E-06; mr1417 (All); LR P-value: 2.77E-06; mr1442 (All); LR P-value: 9.78E-09; mr1453 (All); LR P-value: 4.34E-07; mr1496 (All); LR P-value: 6.56E-15; mr1545 (All); LR P-value: 2.12E-06; mr1574 (All); LR P-value: 4.32E-06; mr1589 (All); LR P-value: 2.87E-22; mr1633 (All); LR P-value: 9.28E-06; mr1696 (All); LR P-value: 3.22E-10; mr1706 (All); LR P-value: 7.53E-08; mr1730 (All); LR P-value: 2.60E-10; mr1762 (All); LR P-value: 6.09E-08; mr1774 (All); LR P-value: 7.26E-06; mr1777 (All); LR P-value: 2.02E-06; mr1858 (All); LR P-value: 1.43E-26; mr1859 (All); LR P-value: 1.31E-26; mr1866 (All); LR P-value: 1.58E-10; mr1868 (All); LR P-value: 1.46E-25; mr1989 (All); LR P-value: 9.97E-08; mr1740_2 (All); LR P-value: 1.09E-06; mr1741_2 (All); LR P-value: 5.59E-10 |
LOC_Os03g50900.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 46.112; most accessible tissue: Callus, score: 72.788 |
| vg0329078127 (J) | chr03 | 29078127 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os03g50900.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os03g50885.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 45.458; most accessible tissue: Callus, score: 72.788 |
| vg0329078200 (J) | chr03 | 29078200 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os03g50900.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os03g50885.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 47.392; most accessible tissue: Callus, score: 85.421 |
| vg0329078357 (J) | chr03 | 29078357 | C | T | 95.00% | 0.00% | C -> T | NA |
LOC_Os03g50900.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 45.644; most accessible tissue: Zhenshan97 young leaf, score: 64.205 |
| vg0329078447 (J) | chr03 | 29078447 | T | C | 91.30% | 0.00% | T -> C |
mr1073 (All); LR P-value: 1.02E-08;
mr1098 (All); LR P-value: 1.04E-32; mr1099 (All); LR P-value: 7.24E-31; mr1101 (All); LR P-value: 4.10E-28; mr1113 (All); LR P-value: 6.33E-15; mr1117 (All); LR P-value: 3.30E-20; mr1119 (All); LR P-value: 6.20E-17; mr1120 (All); LR P-value: 1.13E-22; mr1123 (All); LR P-value: 5.30E-26; mr1146 (All); LR P-value: 7.15E-16; mr1153 (All); LR P-value: 7.36E-06; mr1166 (All); LR P-value: 2.23E-13; mr1231 (All); LR P-value: 4.16E-13; mr1232 (All); LR P-value: 1.91E-11; mr1247 (All); LR P-value: 4.02E-22; mr1312 (All); LR P-value: 3.08E-06; mr1320 (All); LR P-value: 6.27E-07; mr1348 (All); LR P-value: 8.04E-09; mr1365 (All); LR P-value: 8.72E-07; mr1382 (All); LR P-value: 2.25E-06; mr1393 (All); LR P-value: 3.97E-06; mr1417 (All); LR P-value: 4.08E-06; mr1424 (All); LR P-value: 6.81E-06; mr1442 (All); LR P-value: 3.55E-08; mr1496 (All); LR P-value: 7.06E-15; mr1512 (All); LR P-value: 5.70E-06; mr1515 (All); LR P-value: 1.62E-18; mr1523 (All); LR P-value: 6.68E-07; mr1545 (All); LR P-value: 3.80E-06; mr1574 (All); LR P-value: 1.48E-06; mr1589 (All); LR P-value: 3.92E-23; mr1612 (All); LR P-value: 8.14E-12; mr1633 (All); LR P-value: 8.38E-06; mr1696 (All); LR P-value: 3.23E-11; mr1706 (All); LR P-value: 4.03E-07; mr1730 (All); LR P-value: 1.38E-12; mr1762 (All); LR P-value: 8.02E-07; mr1774 (All); LR P-value: 7.51E-06; mr1777 (All); LR P-value: 9.12E-07; mr1858 (All); LR P-value: 5.23E-27; mr1859 (All); LR P-value: 4.78E-27; mr1866 (All); LR P-value: 6.53E-09; mr1868 (All); LR P-value: 7.46E-26; mr1961 (All); LR P-value: 1.21E-18; mr1989 (All); LR P-value: 1.75E-07; mr1740_2 (All); LR P-value: 1.37E-06; mr1741_2 (All); LR P-value: 2.27E-09; mr1846_2 (All); LR P-value: 1.72E-13 |
LOC_Os03g50900.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 51.670; most accessible tissue: Callus, score: 73.245 |
| vg0329078617 (J) | chr03 | 29078617 | T | C | 99.90% | 0.00% | T -> C | NA |
LOC_Os03g50900.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os03g50885.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 55.539; most accessible tissue: Zhenshan97 flower, score: 66.020 |
| vg0329078918 (J) | chr03 | 29078918 | T | G | 95.00% | 0.00% | T -> G | NA |
LOC_Os03g50900.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 53.858; most accessible tissue: Zhenshan97 flower, score: 64.723 |
| vg0329079212 (J) | chr03 | 29079212 | C | T | 99.30% | 0.00% | C -> T | NA |
LOC_Os03g50900.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os03g50885.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 51.430; most accessible tissue: Callus, score: 77.913 |
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