5 variations found. LOC_Os09g24880 (retrotransposon protein; putative; unclassified), ranging from 14,860,622 bp to 14,861,186 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0914860628 (J) | chr09 | 14860628 | G | Unkown | 98.80% | 0.55% | G -> T | NA |
LOC_Os09g24880.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os09g24890.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 53.185; most accessible tissue: Zhenshan97 young leaf, score: 65.804 |
| vg0914860631 (J) | chr09 | 14860631 | T | Unkown | 99.10% | 0.47% | T -> C | NA |
LOC_Os09g24880.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os09g24890.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 53.355; most accessible tissue: Zhenshan97 young leaf, score: 65.804 |
| vg0914860641 (J) | chr09 | 14860641 | T | C | 64.20% | 0.00% | C -> T |
mr1008 (All); LR P-value: 3.06E-102;
mr1014 (All); LR P-value: 2.94E-68; mr1019 (All); LR P-value: 3.65E-56; mr1024 (All); LR P-value: 8.33E-26; mr1074 (All); LR P-value: 5.37E-31; mr1081 (All); LR P-value: 2.10E-35; mr1084 (All); LR P-value: 9.13E-11; mr1092 (All); LR P-value: 2.37E-48; mr1097 (All); LR P-value: 2.98E-09; mr1102 (All); LR P-value: 3.34E-20; mr1133 (All); LR P-value: 2.43E-17; mr1134 (All); LR P-value: 5.59E-82; mr1135 (All); LR P-value: 1.49E-77; mr1146 (All); LR P-value: 1.40E-15; mr1148 (All); LR P-value: 4.54E-27; mr1150 (All); LR P-value: 6.75E-22; mr1152 (All); LR P-value: 1.25E-48; mr1154 (All); LR P-value: 4.18E-54; mr1172 (All); LR P-value: 7.43E-11; mr1205 (All); LR P-value: 1.38E-12; mr1222 (All); LR P-value: 1.18E-07; mr1256 (All); LR P-value: 5.03E-30; mr1276 (All); LR P-value: 3.70E-15; mr1302 (All); LR P-value: 1.08E-08; mr1315 (All); LR P-value: 1.52E-06; mr1322 (All); LR P-value: 3.01E-09; mr1323 (All); LR P-value: 3.89E-16; mr1324 (All); LR P-value: 4.86E-17; mr1326 (All); LR P-value: 6.39E-13; mr1333 (All); LR P-value: 1.31E-34; mr1335 (All); LR P-value: 2.84E-14; mr1361 (All); LR P-value: 2.42E-14; mr1392 (All); LR P-value: 1.34E-06; mr1420 (All); LR P-value: 5.90E-07; mr1488 (All); LR P-value: 1.15E-08; mr1504 (All); LR P-value: 2.45E-91; mr1506 (All); LR P-value: 3.43E-08; mr1517 (All); LR P-value: 1.41E-87; mr1601 (All); LR P-value: 6.21E-40; mr1604 (All); LR P-value: 1.02E-07; mr1623 (All); LR P-value: 3.11E-10; mr1645 (All); LR P-value: 3.38E-39; mr1646 (All); LR P-value: 2.42E-06; mr1647 (All); LR P-value: 4.16E-31; mr1670 (All); LR P-value: 4.37E-34; mr1672 (All); LR P-value: 1.06E-82; mr1682 (All); LR P-value: 7.30E-38; mr1683 (All); LR P-value: 2.96E-11; mr1686 (All); LR P-value: 1.31E-29; mr1695 (All); LR P-value: 1.72E-61; mr1711 (All); LR P-value: 4.32E-64; mr1723 (All); LR P-value: 1.01E-27; mr1754 (All); LR P-value: 1.03E-19; mr1758 (All); LR P-value: 1.09E-86; mr1764 (All); LR P-value: 5.74E-08; mr1767 (All); LR P-value: 5.72E-18; mr1775 (All); LR P-value: 1.62E-10; mr1776 (All); LR P-value: 1.80E-08; mr1797 (All); LR P-value: 4.27E-07; mr1801 (All); LR P-value: 4.27E-07; mr1838 (All); LR P-value: 1.68E-20; mr1839 (All); LR P-value: 7.50E-22; mr1865 (All); LR P-value: 1.41E-75; mr1873 (All); LR P-value: 1.04E-39; mr1889 (All); LR P-value: 1.06E-53; mr1896 (All); LR P-value: 3.07E-69; mr1917 (All); LR P-value: 7.87E-25; mr1922 (All); LR P-value: 2.04E-30; mr1924 (All); LR P-value: 2.34E-13; mr1987 (All); LR P-value: 2.53E-112; mr1074_2 (All); LR P-value: 1.46E-26; mr1081_2 (All); LR P-value: 1.11E-32; mr1082_2 (All); LR P-value: 3.20E-35; mr1092_2 (All); LR P-value: 3.04E-41; mr1103_2 (All); LR P-value: 3.36E-68; mr1146_2 (All); LR P-value: 5.96E-17; mr1150_2 (All); LR P-value: 7.06E-33; mr1152_2 (All); LR P-value: 1.71E-40; mr1154_2 (All); LR P-value: 4.16E-53; mr1181_2 (All); LR P-value: 5.24E-35; mr1256_2 (All); LR P-value: 2.04E-33; mr1324_2 (All); LR P-value: 1.92E-15; mr1333_2 (All); LR P-value: 1.72E-14; mr1342_2 (All); LR P-value: 1.05E-16; mr1386_2 (All); LR P-value: 1.54E-22; mr1657_2 (All); LR P-value: 2.14E-18; mr1733_2 (All); LR P-value: 8.91E-62; mr1861_2 (All); LR P-value: 2.78E-48; mr1865_2 (All); LR P-value: 2.85E-95 |
LOC_Os09g24880.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 53.397; most accessible tissue: Zhenshan97 young leaf, score: 65.280 |
| vg0914860711 (J) | chr09 | 14860711 | G | GA | 99.90% | 0.00% | G -> GA | NA |
The average chromatin accessibility score: 55.551; most accessible tissue: Callus, score: 82.969
|
| vg0914860717 (J) | chr09 | 14860717 | A | T | 99.60% | 0.00% | A -> T | NA |
LOC_Os09g24880.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 57.572; most accessible tissue: Callus, score: 82.969 |