10 variations found. LOC_Os05g45060 (RING-H2 finger protein ATL2M; putative; expressed), ranging from 26,186,579 bp to 26,187,486 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0526186721 (J) | chr05 | 26186721 | C | CGCG | 57.90% | 1.48% | CGCG -> C | NA |
LOC_Os05g45060.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g45060.1 Alt: C| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 95.439; most accessible tissue: Zhenshan97 flag leaf, score: 98.062 |
| vg0526186724 (J) | chr05 | 26186724 | G | C | 73.60% | 6.09% | G -> C | NA |
LOC_Os05g45060.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g45060.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 95.405; most accessible tissue: Zhenshan97 flag leaf, score: 98.047 |
| vg0526186949 (J) | chr05 | 26186949 | G | A | 63.80% | 0.00% | A -> G |
mr1032 (Ind_All); LR P-value: 6.30E-06;
mr1059 (All); LR P-value: 1.05E-14; mr1105 (All); LR P-value: 5.71E-40; mr1141 (All); LR P-value: 3.46E-43; mr1167 (All); LR P-value: 2.48E-15; mr1194 (All); LR P-value: 9.06E-44; mr1726 (All); LR P-value: 2.30E-13; mr1828 (All); LR P-value: 2.51E-35; mr1889 (All); LR P-value: 1.18E-56; mr1889 (Ind_All); LR P-value: 2.32E-09; mr1896 (All); LR P-value: 2.49E-78; mr1896 (Ind_All); LR P-value: 2.98E-11; mr1903 (All); LR P-value: 5.52E-31; mr1903 (Ind_All); LR P-value: 1.64E-10; mr1905 (All); LR P-value: 1.71E-10; mr1907 (All); LR P-value: 2.10E-87; mr1907 (Ind_All); LR P-value: 2.55E-13; mr1915 (All); LR P-value: 1.40E-07; mr1934 (All); LR P-value: 1.18E-88; mr1934 (Ind_All); LMM P-value: 1.71E-06; LR P-value: 7.43E-13; mr1935 (All); LR P-value: 5.88E-65; mr1935 (Ind_All); LR P-value: 2.14E-11; mr1938 (All); LR P-value: 6.21E-12; mr1030_2 (All); LR P-value: 2.37E-07; mr1105_2 (All); LR P-value: 2.54E-34; mr1141_2 (All); LR P-value: 3.04E-55; mr1162_2 (All); LR P-value: 2.82E-15; mr1175_2 (All); LR P-value: 7.15E-23; mr1193_2 (Ind_All); LR P-value: 5.18E-06; mr1195_2 (All); LR P-value: 1.79E-20; mr1195_2 (Ind_All); LR P-value: 4.81E-11; mr1349_2 (All); LR P-value: 2.57E-10; mr1402_2 (All); LR P-value: 8.06E-62; mr1478_2 (All); LR P-value: 1.67E-08; mr1478_2 (Ind_All); LR P-value: 2.26E-06; mr1546_2 (All); LR P-value: 9.26E-49; mr1588_2 (All); LR P-value: 4.79E-25; mr1599_2 (All); LR P-value: 1.05E-58; mr1821_2 (All); LR P-value: 2.66E-07; mr1828_2 (All); LMM P-value: 4.16E-12; LR P-value: 1.23E-87; mr1828_2 (Ind_All); LMM P-value: 2.33E-12; LR P-value: 6.09E-19; mr1837_2 (All); LR P-value: 2.79E-07; mr1889_2 (All); LR P-value: 3.71E-69; mr1889_2 (Ind_All); LR P-value: 1.31E-09; mr1896_2 (All); LR P-value: 6.17E-69; mr1896_2 (Ind_All); LR P-value: 1.38E-08; mr1907_2 (All); LR P-value: 1.14E-102; mr1907_2 (Ind_All); LR P-value: 1.24E-15; mr1915_2 (All); LR P-value: 1.79E-06; mr1934_2 (All); LR P-value: 4.20E-96; mr1934_2 (Ind_All); LR P-value: 4.32E-14; mr1938_2 (All); LR P-value: 6.83E-16; mr1938_2 (Ind_All); LR P-value: 3.97E-07 |
LOC_Os05g45060.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 94.603; most accessible tissue: Zhenshan97 panicle, score: 97.905 |
| vg0526187029 (J) | chr05 | 26187029 | G | C | 99.60% | 0.00% | G -> C | NA |
LOC_Os05g45060.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os05g45050.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os05g45050.2 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os05g45070.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 94.116; most accessible tissue: Zhenshan97 panicle, score: 97.620 |
| vg0526187086 (J) | chr05 | 26187086 | A | G | 61.80% | 0.00% | G -> A |
mr1105 (All); LR P-value: 1.17E-36;
mr1478 (All); LR P-value: 6.31E-14; mr1842 (All); LR P-value: 5.24E-16; mr1889 (All); LR P-value: 1.97E-61; mr1896 (All); LR P-value: 1.23E-78; mr1896 (Ind_All); LR P-value: 3.29E-10; mr1902 (All); LR P-value: 1.90E-11; mr1903 (All); LR P-value: 2.29E-30; mr1903 (Ind_All); LR P-value: 5.64E-09; mr1907 (All); LR P-value: 5.38E-88; mr1907 (Ind_All); LR P-value: 3.48E-12; mr1915 (All); LR P-value: 6.19E-07; mr1934 (All); LR P-value: 1.91E-83; mr1934 (Ind_All); LR P-value: 3.67E-11; mr1935 (All); LR P-value: 1.18E-59; mr1935 (Ind_All); LR P-value: 8.80E-10; mr1162_2 (All); LR P-value: 1.42E-16; mr1175_2 (All); LR P-value: 2.20E-22; mr1195_2 (All); LR P-value: 2.12E-23; mr1195_2 (Ind_All); LR P-value: 4.83E-10; mr1281_2 (All); LR P-value: 1.79E-18; mr1349_2 (All); LR P-value: 9.89E-10; mr1478_2 (Ind_All); LR P-value: 4.29E-06; mr1546_2 (All); LR P-value: 1.39E-45; mr1588_2 (All); LR P-value: 8.44E-25; mr1592_2 (All); LR P-value: 1.07E-16; mr1654_2 (All); LR P-value: 4.06E-07; mr1713_2 (All); LR P-value: 2.99E-13; mr1722_2 (All); LR P-value: 2.16E-11; mr1756_2 (All); LR P-value: 6.43E-10; mr1790_2 (All); LR P-value: 1.06E-16; mr1828_2 (All); LMM P-value: 5.64E-08; LR P-value: 5.71E-73; mr1828_2 (Ind_All); LMM P-value: 1.82E-10; LR P-value: 1.79E-16; mr1837_2 (All); LR P-value: 3.56E-07; mr1842_2 (All); LR P-value: 4.71E-17; mr1889_2 (All); LR P-value: 4.11E-70; mr1889_2 (Ind_All); LR P-value: 5.24E-09; mr1896_2 (All); LR P-value: 3.79E-67; mr1896_2 (Ind_All); LR P-value: 1.09E-07; mr1907_2 (All); LR P-value: 2.37E-100; mr1907_2 (Ind_All); LR P-value: 4.04E-15; mr1915_2 (All); LR P-value: 1.58E-06; mr1933_2 (All); LR P-value: 4.88E-23; mr1934_2 (All); LR P-value: 1.79E-85; mr1934_2 (Ind_All); LR P-value: 1.74E-13; mr1938_2 (All); LR P-value: 1.39E-15; mr1938_2 (Ind_All); LR P-value: 2.07E-06; mr1947_2 (All); LR P-value: 7.50E-09 |
LOC_Os05g45060.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 92.492; most accessible tissue: Zhenshan97 panicle, score: 97.121 |
| vg0526187240 (J) | chr05 | 26187240 | G | GT | 64.00% | 0.00% | GT -> G | NA |
LOC_Os05g45060.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g45050.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g45050.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g45070.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 90.485; most accessible tissue: Callus, score: 95.224 |
| vg0526187297 (J) | chr05 | 26187297 | C | T | 63.90% | 0.00% | T -> C |
mr1032 (All); LR P-value: 1.20E-13;
mr1032 (Ind_All); LR P-value: 6.30E-06; mr1059 (All); LR P-value: 4.57E-15; mr1105 (All); LR P-value: 5.42E-40; mr1122 (All); LR P-value: 3.16E-22; mr1165 (All); LR P-value: 4.55E-15; mr1167 (All); LR P-value: 6.82E-16; mr1194 (All); LR P-value: 3.44E-43; mr1477 (All); LR P-value: 2.62E-20; mr1478 (All); LR P-value: 5.07E-14; mr1535 (All); LR P-value: 1.17E-14; mr1675 (All); LR P-value: 4.78E-15; mr1726 (All); LR P-value: 1.54E-13; mr1828 (All); LR P-value: 1.77E-34; mr1889 (All); LR P-value: 3.55E-57; mr1889 (Ind_All); LR P-value: 2.32E-09; mr1896 (All); LR P-value: 9.28E-81; mr1896 (Ind_All); LR P-value: 2.98E-11; mr1903 (All); LR P-value: 4.86E-33; mr1903 (Ind_All); LR P-value: 1.64E-10; mr1907 (All); LR P-value: 1.88E-90; mr1907 (Ind_All); LR P-value: 2.55E-13; mr1915 (All); LR P-value: 1.69E-07; mr1934 (All); LMM P-value: 1.74E-06; LR P-value: 3.82E-92; mr1934 (Ind_All); LMM P-value: 1.71E-06; LR P-value: 7.43E-13; mr1935 (All); LMM P-value: 4.90E-06; LR P-value: 8.83E-67; mr1935 (Ind_All); LR P-value: 2.14E-11; mr1938 (All); LR P-value: 5.64E-12; mr1944 (All); LR P-value: 1.21E-34; mr1969 (All); LR P-value: 1.93E-14; mr1995 (All); LR P-value: 1.06E-16; mr1030_2 (All); LR P-value: 1.84E-07; mr1105_2 (All); LR P-value: 1.36E-34; mr1141_2 (All); LR P-value: 1.90E-53; mr1162_2 (All); LR P-value: 2.72E-15; mr1175_2 (All); LR P-value: 2.32E-22; mr1193_2 (Ind_All); LR P-value: 5.18E-06; mr1195_2 (All); LR P-value: 5.48E-21; mr1195_2 (Ind_All); LR P-value: 4.81E-11; mr1253_2 (All); LR P-value: 1.07E-21; mr1349_2 (All); LR P-value: 4.24E-10; mr1478_2 (All); LR P-value: 4.77E-09; mr1478_2 (Ind_All); LR P-value: 2.26E-06; mr1546_2 (All); LR P-value: 1.20E-50; mr1588_2 (All); LR P-value: 5.23E-25; mr1599_2 (All); LR P-value: 2.52E-60; mr1828_2 (All); LMM P-value: 9.27E-14; LR P-value: 2.28E-89; mr1828_2 (Ind_All); LMM P-value: 2.33E-12; LR P-value: 6.09E-19; mr1889_2 (All); LR P-value: 5.39E-71; mr1889_2 (Ind_All); LR P-value: 1.31E-09; mr1896_2 (All); LR P-value: 5.57E-72; mr1896_2 (Ind_All); LR P-value: 1.38E-08; mr1907_2 (All); LR P-value: 7.97E-107; mr1907_2 (Ind_All); LR P-value: 1.24E-15; mr1934_2 (All); LR P-value: 6.88E-100; mr1934_2 (Ind_All); LR P-value: 4.32E-14; mr1938_2 (All); LR P-value: 1.99E-15; mr1938_2 (Ind_All); LR P-value: 3.97E-07 |
LOC_Os05g45060.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g45050.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g45050.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g45070.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 87.790; most accessible tissue: Callus, score: 95.224 |
| vg0526187315 (J) | chr05 | 26187315 | C | T | 63.90% | 0.00% | T -> C |
mr1032 (All); LR P-value: 6.71E-14;
mr1032 (Ind_All); LR P-value: 6.30E-06; mr1059 (All); LR P-value: 1.77E-15; mr1105 (All); LR P-value: 2.03E-39; mr1122 (All); LR P-value: 1.33E-21; mr1143 (All); LR P-value: 1.62E-15; mr1165 (All); LR P-value: 3.11E-15; mr1167 (All); LR P-value: 2.46E-16; mr1477 (All); LR P-value: 1.00E-20; mr1478 (All); LR P-value: 2.57E-14; mr1535 (All); LR P-value: 2.99E-15; mr1675 (All); LR P-value: 1.50E-15; mr1726 (All); LR P-value: 4.37E-14; mr1889 (All); LR P-value: 1.93E-56; mr1889 (Ind_All); LR P-value: 2.32E-09; mr1896 (All); LR P-value: 1.98E-79; mr1896 (Ind_All); LR P-value: 2.98E-11; mr1903 (All); LR P-value: 5.49E-32; mr1903 (Ind_All); LR P-value: 1.64E-10; mr1907 (All); LR P-value: 1.64E-89; mr1907 (Ind_All); LR P-value: 2.55E-13; mr1915 (All); LR P-value: 1.94E-07; mr1934 (All); LMM P-value: 6.85E-06; LR P-value: 1.04E-90; mr1934 (Ind_All); LMM P-value: 1.71E-06; LR P-value: 7.43E-13; mr1935 (All); LR P-value: 7.52E-66; mr1935 (Ind_All); LR P-value: 2.14E-11; mr1938 (All); LR P-value: 6.08E-12; mr1944 (All); LR P-value: 2.58E-34; mr1950 (All); LR P-value: 7.46E-15; mr1969 (All); LR P-value: 7.25E-15; mr1995 (All); LR P-value: 1.69E-17; mr1030_2 (All); LR P-value: 1.31E-07; mr1105_2 (All); LR P-value: 3.20E-34; mr1162_2 (All); LR P-value: 5.83E-15; mr1175_2 (All); LR P-value: 1.53E-22; mr1193_2 (Ind_All); LR P-value: 5.18E-06; mr1195_2 (All); LR P-value: 4.53E-21; mr1195_2 (Ind_All); LR P-value: 4.81E-11; mr1253_2 (All); LR P-value: 3.84E-21; mr1349_2 (All); LR P-value: 1.02E-09; mr1478_2 (All); LR P-value: 2.05E-09; mr1478_2 (Ind_All); LR P-value: 2.26E-06; mr1546_2 (All); LR P-value: 7.38E-51; mr1588_2 (All); LR P-value: 1.26E-24; mr1599_2 (All); LR P-value: 1.65E-59; mr1828_2 (All); LMM P-value: 1.64E-12; LR P-value: 1.12E-87; mr1828_2 (Ind_All); LMM P-value: 2.33E-12; LR P-value: 6.09E-19; mr1889_2 (All); LR P-value: 2.01E-70; mr1889_2 (Ind_All); LR P-value: 1.31E-09; mr1896_2 (All); LR P-value: 2.01E-71; mr1896_2 (Ind_All); LR P-value: 1.38E-08; mr1907_2 (All); LR P-value: 2.83E-106; mr1907_2 (Ind_All); LR P-value: 1.24E-15; mr1934_2 (All); LR P-value: 9.45E-99; mr1934_2 (Ind_All); LR P-value: 4.32E-14; mr1938_2 (All); LR P-value: 4.06E-15; mr1938_2 (Ind_All); LR P-value: 3.97E-07; mr1971_2 (All); LR P-value: 1.03E-21 |
LOC_Os05g45060.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g45050.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g45050.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g45070.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 86.688; most accessible tissue: Callus, score: 95.224 |
| vg0526187402 (J) | chr05 | 26187402 | G | A | 63.80% | 0.00% | A -> G |
mr1032 (Ind_All); LR P-value: 6.30E-06;
mr1059 (All); LR P-value: 7.55E-15; mr1105 (All); LR P-value: 7.83E-40; mr1122 (All); LR P-value: 5.20E-22; mr1167 (All); LR P-value: 1.43E-15; mr1194 (All); LR P-value: 1.81E-43; mr1535 (All); LR P-value: 1.57E-14; mr1675 (All); LR P-value: 5.85E-15; mr1726 (All); LR P-value: 1.36E-13; mr1889 (All); LR P-value: 2.50E-58; mr1889 (Ind_All); LR P-value: 2.32E-09; mr1896 (All); LR P-value: 3.97E-80; mr1896 (Ind_All); LR P-value: 2.98E-11; mr1903 (All); LR P-value: 2.24E-32; mr1903 (Ind_All); LR P-value: 1.64E-10; mr1907 (All); LR P-value: 3.10E-88; mr1907 (Ind_All); LR P-value: 2.55E-13; mr1915 (All); LR P-value: 1.06E-07; mr1934 (All); LR P-value: 4.40E-89; mr1934 (Ind_All); LMM P-value: 1.71E-06; LR P-value: 7.43E-13; mr1935 (All); LR P-value: 2.51E-65; mr1935 (Ind_All); LR P-value: 2.14E-11; mr1938 (All); LR P-value: 6.21E-12; mr1995 (All); LR P-value: 2.23E-16; mr1030_2 (All); LR P-value: 1.30E-07; mr1105_2 (All); LR P-value: 2.82E-33; mr1141_2 (All); LR P-value: 4.58E-55; mr1162_2 (All); LR P-value: 1.33E-15; mr1175_2 (All); LR P-value: 1.65E-23; mr1193_2 (Ind_All); LR P-value: 5.18E-06; mr1195_2 (All); LR P-value: 3.58E-21; mr1195_2 (Ind_All); LR P-value: 4.81E-11; mr1253_2 (All); LR P-value: 7.38E-21; mr1349_2 (All); LR P-value: 2.16E-10; mr1358_2 (All); LR P-value: 1.33E-06; mr1402_2 (All); LR P-value: 4.63E-61; mr1478_2 (Ind_All); LR P-value: 2.26E-06; mr1546_2 (All); LR P-value: 1.20E-49; mr1588_2 (All); LR P-value: 2.39E-25; mr1599_2 (All); LR P-value: 5.11E-60; mr1637_2 (All); LR P-value: 9.19E-19; mr1780_2 (All); LR P-value: 2.39E-32; mr1790_2 (All); LR P-value: 2.39E-14; mr1821_2 (All); LR P-value: 2.84E-07; mr1828_2 (All); LMM P-value: 2.99E-13; LR P-value: 1.54E-88; mr1828_2 (Ind_All); LMM P-value: 2.33E-12; LR P-value: 6.09E-19; mr1837_2 (All); LR P-value: 8.12E-08; mr1889_2 (All); LR P-value: 1.77E-68; mr1889_2 (Ind_All); LR P-value: 1.31E-09; mr1896_2 (All); LR P-value: 1.21E-68; mr1896_2 (Ind_All); LR P-value: 1.38E-08; mr1907_2 (All); LR P-value: 4.22E-102; mr1907_2 (Ind_All); LR P-value: 1.24E-15; mr1915_2 (All); LR P-value: 8.29E-07; mr1934_2 (All); LR P-value: 8.49E-95; mr1934_2 (Ind_All); LR P-value: 4.32E-14; mr1938_2 (All); LR P-value: 2.07E-16; mr1938_2 (Ind_All); LR P-value: 3.97E-07 |
LOC_Os05g45060.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g45070.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.176; most accessible tissue: Minghui63 flower, score: 89.149 |
| vg0526187451 (J) | chr05 | 26187451 | G | GT | 36.40% | 32.56% | G -> GT | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g45060.1 Alt: GT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g45070.1 Alt: GT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 79.922; most accessible tissue: Callus, score: 94.934 |