15 variations found. LOC_Os05g42000 (peroxidase precursor; putative; expressed), ranging from 24,587,144 bp to 24,589,539 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0524587148 (J) | chr05 | 24587148 | T | G | 55.80% | 0.19% | G -> T |
mr1020 (All); LR P-value: 1.89E-21;
mr1032 (All); LR P-value: 1.62E-16; mr1032 (Ind_All); LR P-value: 6.60E-06; mr1165 (All); LR P-value: 1.45E-16; mr1189 (All); LR P-value: 6.60E-06; mr1478 (All); LR P-value: 3.95E-16; mr1796 (All); LR P-value: 1.00E-06; mr1889 (All); LMM P-value: 8.32E-10; LR P-value: 2.76E-58; mr1889 (Ind_All); LMM P-value: 3.07E-16; LR P-value: 5.70E-32; mr1896 (All); LMM P-value: 7.16E-10; LR P-value: 1.78E-68; mr1896 (Ind_All); LMM P-value: 2.99E-16; LR P-value: 1.95E-30; mr1903 (All); LMM P-value: 3.52E-13; LR P-value: 3.52E-30; mr1903 (Ind_All); LMM P-value: 1.72E-18; LR P-value: 1.82E-32; mr1907 (All); LMM P-value: 5.58E-15; LR P-value: 2.01E-88; mr1907 (Ind_All); LMM P-value: 2.25E-23; LR P-value: 3.38E-48; mr1934 (All); LMM P-value: 1.20E-14; mr1934 (Ind_All); LMM P-value: 1.71E-20; LR P-value: 6.68E-39; mr1935 (All); LMM P-value: 6.05E-10; mr1935 (Ind_All); LMM P-value: 1.00E-14; LR P-value: 3.28E-28; mr1109_2 (All); LR P-value: 2.56E-57; mr1332_2 (Ind_All); LR P-value: 5.27E-06; mr1428_2 (Ind_All); LR P-value: 2.85E-06; mr1478_2 (All); LR P-value: 1.66E-08; mr1540_2 (Ind_All); LR P-value: 4.26E-06; mr1612_2 (All); LMM P-value: 9.35E-06; LR P-value: 7.43E-11; mr1715_2 (Ind_All); LR P-value: 1.01E-10; mr1889_2 (All); LMM P-value: 1.70E-07; LR P-value: 6.67E-69; mr1889_2 (Ind_All); LMM P-value: 2.02E-10; LR P-value: 7.19E-26; mr1896_2 (All); LMM P-value: 4.52E-09; LR P-value: 7.30E-67; mr1896_2 (Ind_All); LMM P-value: 3.54E-13; LR P-value: 4.26E-25; mr1907_2 (All); LMM P-value: 9.30E-13; LR P-value: 2.19E-95; mr1907_2 (Ind_All); LMM P-value: 3.58E-16; LR P-value: 5.45E-36; mr1934_2 (All); LMM P-value: 2.36E-12; mr1934_2 (Ind_All); LMM P-value: 6.78E-17; LR P-value: 9.78E-35 |
LOC_Os05g42000.1 Alt: T| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os05g42000.2 Alt: T| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os05g42000.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g42000.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41990.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g42010.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g42010.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 96.626; most accessible tissue: Zhenshan97 young leaf, score: 99.105 |
| vg0524587173 (J) | chr05 | 24587173 | G | A | 99.00% | 0.00% | G -> A | NA |
LOC_Os05g42000.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g42000.2 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41990.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g42010.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g42010.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 96.703; most accessible tissue: Zhenshan97 young leaf, score: 99.130 |
| vg0524587185 (J) | chr05 | 24587185 | A | G | 61.60% | 0.00% | G -> A |
mr1059 (All); LR P-value: 4.09E-15;
mr1066 (All); LR P-value: 8.92E-06; mr1122 (All); LR P-value: 6.56E-27; mr1141 (All); LR P-value: 4.99E-45; mr1150 (All); LR P-value: 8.16E-22; mr1167 (All); LR P-value: 1.98E-15; mr1272 (All); LR P-value: 8.55E-11; mr1535 (All); LR P-value: 3.28E-15; mr1726 (All); LR P-value: 2.36E-14; mr1846 (All); LR P-value: 9.10E-12; mr1889 (All); LMM P-value: 1.12E-20; LR P-value: 3.64E-85; mr1889 (Ind_All); LMM P-value: 6.74E-19; LR P-value: 7.68E-34; mr1896 (All); LMM P-value: 1.36E-23; LR P-value: 1.62E-110; mr1896 (Ind_All); LMM P-value: 2.10E-22; LR P-value: 1.10E-35; mr1903 (All); LMM P-value: 2.27E-26; LR P-value: 7.80E-57; mr1903 (Ind_All); LMM P-value: 2.36E-24; LR P-value: 8.75E-38; mr1907 (All); LMM P-value: 1.13E-31; LR P-value: 1.33E-138; mr1907 (Ind_All); LMM P-value: 7.61E-29; LR P-value: 1.85E-54; mr1934 (All); LMM P-value: 4.01E-28; LR P-value: 1.50E-130; mr1934 (Ind_All); LMM P-value: 2.00E-23; LR P-value: 4.18E-42; mr1935 (All); LMM P-value: 1.26E-25; LR P-value: 1.68E-97; mr1935 (Ind_All); LMM P-value: 1.81E-19; LR P-value: 6.05E-33; mr1995 (All); LR P-value: 1.31E-16; mr1020_2 (All); LR P-value: 9.13E-07; mr1162_2 (All); LR P-value: 5.67E-17; mr1168_2 (All); LR P-value: 4.27E-20; mr1175_2 (All); LR P-value: 3.93E-23; mr1272_2 (All); LR P-value: 1.78E-06; mr1321_2 (All); LR P-value: 3.73E-07; mr1322_2 (Ind_All); LR P-value: 3.85E-06; mr1332_2 (Ind_All); LR P-value: 1.52E-07; mr1349_2 (All); LR P-value: 2.14E-12; mr1349_2 (Ind_All); LR P-value: 2.88E-06; mr1354_2 (Ind_All); LR P-value: 3.24E-06; mr1355_2 (All); LR P-value: 6.02E-07; mr1428_2 (Ind_All); LR P-value: 3.13E-06; mr1452_2 (All); LR P-value: 1.06E-06; mr1462_2 (All); LR P-value: 7.56E-06; mr1478_2 (All); LR P-value: 1.45E-09; mr1520_2 (All); LR P-value: 1.58E-11; mr1546_2 (All); LR P-value: 3.78E-49; mr1576_2 (All); LR P-value: 7.00E-08; mr1607_2 (All); LR P-value: 3.51E-08; mr1712_2 (All); LR P-value: 7.15E-22; mr1715_2 (Ind_All); LR P-value: 4.75E-11; mr1717_2 (All); LR P-value: 2.26E-14; mr1722_2 (All); LR P-value: 2.51E-11; mr1726_2 (All); LR P-value: 6.89E-15; mr1889_2 (All); LMM P-value: 4.12E-19; LR P-value: 1.49E-100; mr1889_2 (Ind_All); LMM P-value: 1.00E-13; LR P-value: 1.67E-31; mr1893_2 (All); LR P-value: 9.33E-12; mr1895_2 (All); LR P-value: 4.46E-07; mr1896_2 (All); LMM P-value: 1.68E-20; LR P-value: 1.26E-99; mr1896_2 (Ind_All); LMM P-value: 4.09E-16; LR P-value: 8.25E-29; mr1899_2 (All); LR P-value: 5.24E-06; mr1907_2 (All); LMM P-value: 4.42E-24; LR P-value: 2.26E-140; mr1907_2 (Ind_All); LMM P-value: 3.57E-22; LR P-value: 2.58E-44; mr1934_2 (All); LMM P-value: 8.85E-27; LR P-value: 2.87E-135; mr1934_2 (Ind_All); LMM P-value: 1.33E-20; LR P-value: 9.22E-40 |
LOC_Os05g42000.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g42000.2 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41990.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g42010.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g42010.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 97.002; most accessible tissue: Zhenshan97 young leaf, score: 99.139 |
| vg0524587252 (J) | chr05 | 24587252 | C | T | 94.70% | 0.00% | C -> T | NA |
LOC_Os05g42000.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g42000.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41990.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g42010.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g42010.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 96.564; most accessible tissue: Zhenshan97 young leaf, score: 98.942 |
| vg0524587275 (J) | chr05 | 24587275 | T | C | 55.80% | 0.00% | C -> T |
mr1020 (All); LR P-value: 9.94E-22;
mr1032 (All); LR P-value: 8.42E-17; mr1032 (Ind_All); LR P-value: 6.52E-06; mr1109 (All); LR P-value: 1.61E-46; mr1165 (All); LR P-value: 1.03E-16; mr1189 (All); LR P-value: 5.89E-06; mr1478 (All); LR P-value: 2.85E-16; mr1796 (All); LR P-value: 8.27E-07; mr1889 (All); LMM P-value: 4.99E-10; LR P-value: 2.02E-58; mr1889 (Ind_All); LMM P-value: 2.46E-16; LR P-value: 5.10E-32; mr1896 (All); LMM P-value: 4.15E-11; LR P-value: 2.40E-70; mr1896 (Ind_All); LMM P-value: 2.60E-16; LR P-value: 1.66E-30; mr1903 (All); LMM P-value: 1.26E-14; LR P-value: 1.81E-31; mr1903 (Ind_All); LMM P-value: 1.85E-18; LR P-value: 1.66E-32; mr1907 (All); LMM P-value: 4.11E-15; LR P-value: 9.16E-89; mr1907 (Ind_All); LMM P-value: 1.58E-23; LR P-value: 2.45E-48; mr1934 (All); LMM P-value: 1.01E-14; mr1934 (Ind_All); LMM P-value: 1.39E-20; LR P-value: 5.50E-39; mr1935 (All); LMM P-value: 3.86E-11; mr1935 (Ind_All); LMM P-value: 4.99E-15; LR P-value: 2.09E-28; mr1971 (All); LR P-value: 8.23E-21; mr1109_2 (All); LMM P-value: 7.03E-06; LR P-value: 8.28E-58; mr1332_2 (Ind_All); LR P-value: 5.71E-06; mr1349_2 (All); LR P-value: 1.13E-09; mr1428_2 (Ind_All); LR P-value: 3.05E-06; mr1478_2 (All); LR P-value: 8.92E-09; mr1540_2 (Ind_All); LR P-value: 4.58E-06; mr1612_2 (All); LMM P-value: 3.62E-06; LR P-value: 5.00E-11; mr1715_2 (Ind_All); LR P-value: 9.78E-11; mr1889_2 (All); LMM P-value: 1.01E-07; LR P-value: 5.00E-69; mr1889_2 (Ind_All); LMM P-value: 1.44E-10; LR P-value: 6.55E-26; mr1896_2 (All); LMM P-value: 7.04E-10; LR P-value: 9.12E-68; mr1896_2 (Ind_All); LMM P-value: 2.10E-13; LR P-value: 2.96E-25; mr1907_2 (All); LMM P-value: 4.51E-13; LR P-value: 3.17E-96; mr1907_2 (Ind_All); LMM P-value: 2.49E-16; LR P-value: 4.23E-36; mr1934_2 (All); LMM P-value: 5.58E-12; mr1934_2 (Ind_All); LMM P-value: 5.26E-17; LR P-value: 8.45E-35; mr1938_2 (All); LR P-value: 6.76E-14 |
LOC_Os05g42000.1 Alt: T| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os05g42000.2 Alt: T| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os05g42000.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g42000.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41990.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g42010.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g42010.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 96.520; most accessible tissue: Zhenshan97 young leaf, score: 98.868 |
| vg0524587581 (J) | chr05 | 24587581 | C | T | 99.70% | 0.00% | C -> T | NA |
LOC_Os05g42000.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os05g42000.2 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 87.227; most accessible tissue: Zhenshan97 flower, score: 95.196 |
| vg0524587903 (J) | chr05 | 24587903 | G | A | 94.60% | 0.00% | G -> A,C |
mr1465 (All); LR P-value: 2.31E-08;
mr1499 (All); LR P-value: 1.42E-10; mr1612 (All); LMM P-value: 8.07E-12; LR P-value: 9.07E-22; mr1706 (All); LR P-value: 6.38E-07; mr1989 (All); LR P-value: 3.73E-09; mr1047_2 (All); LR P-value: 5.09E-10; mr1109_2 (All); LMM P-value: 4.59E-09; mr1126_2 (All); LR P-value: 9.49E-08; mr1166_2 (All); LR P-value: 1.17E-09; mr1612_2 (All); LMM P-value: 8.54E-12; LR P-value: 2.56E-18; mr1815_2 (All); LR P-value: 1.19E-06 |
LOC_Os05g42000.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os05g41990.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g42010.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g42010.2 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g42000.2 Alt: C| intron_variant MODIFIER(snpEff) LOC_Os05g42000.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 84.071; most accessible tissue: Zhenshan97 flower, score: 94.106 |
| vg0524588276 (J) | chr05 | 24588276 | C | G | 55.50% | 0.00% | G -> C |
mr1020 (All); LR P-value: 2.00E-22;
mr1029 (All); LR P-value: 6.91E-06; mr1032 (All); LR P-value: 5.32E-18; mr1165 (All); LR P-value: 2.23E-18; mr1170 (Ind_All); LR P-value: 9.09E-06; mr1189 (All); LR P-value: 4.32E-06; mr1477 (All); LR P-value: 3.33E-20; mr1478 (All); LR P-value: 1.74E-17; mr1638 (All); LR P-value: 1.72E-28; mr1728 (All); LR P-value: 2.53E-06; mr1796 (All); LR P-value: 9.19E-07; mr1889 (All); LMM P-value: 9.61E-13; LR P-value: 2.55E-61; mr1889 (Ind_All); LMM P-value: 6.38E-19; LR P-value: 1.14E-34; mr1896 (All); LMM P-value: 2.52E-13; LR P-value: 1.43E-72; mr1896 (Ind_All); LMM P-value: 8.77E-18; LR P-value: 8.21E-33; mr1903 (All); LMM P-value: 3.55E-16; LR P-value: 1.37E-32; mr1903 (Ind_All); LMM P-value: 2.83E-19; LR P-value: 6.21E-34; mr1907 (All); LMM P-value: 1.42E-17; LR P-value: 5.18E-92; mr1907 (Ind_All); LMM P-value: 2.89E-26; LR P-value: 8.52E-52; mr1934 (All); LMM P-value: 1.22E-15; mr1934 (Ind_All); LMM P-value: 7.15E-20; LR P-value: 4.83E-39; mr1935 (All); LMM P-value: 8.65E-13; mr1935 (Ind_All); LMM P-value: 6.04E-16; LR P-value: 1.11E-29; mr1971 (All); LR P-value: 4.12E-21; mr1322_2 (Ind_All); LR P-value: 8.53E-06; mr1332_2 (Ind_All); LR P-value: 3.12E-06; mr1349_2 (All); LR P-value: 4.12E-10; mr1428_2 (Ind_All); LR P-value: 9.25E-07; mr1478_2 (All); LR P-value: 5.55E-10; mr1612_2 (All); LR P-value: 4.73E-10; mr1655_2 (All); LR P-value: 4.14E-06; mr1715_2 (Ind_All); LR P-value: 1.33E-10; mr1889_2 (All); LMM P-value: 1.72E-09; LR P-value: 9.09E-72; mr1889_2 (Ind_All); LMM P-value: 9.05E-12; LR P-value: 2.37E-28; mr1896_2 (All); LMM P-value: 2.48E-12; LR P-value: 1.05E-70; mr1896_2 (Ind_All); LMM P-value: 1.84E-15; LR P-value: 6.69E-28; mr1899_2 (All); LR P-value: 3.04E-06; mr1907_2 (All); LMM P-value: 6.93E-15; LR P-value: 8.76E-98; mr1907_2 (Ind_All); LMM P-value: 4.39E-18; LR P-value: 1.35E-38; mr1934_2 (All); LMM P-value: 8.28E-13; mr1934_2 (Ind_All); LMM P-value: 4.94E-17; LR P-value: 5.67E-36 |
LOC_Os05g41990.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g42010.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g42010.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g42000.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g42000.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 86.970; most accessible tissue: Zhenshan97 flower, score: 93.098 |
| vg0524588402 (J) | chr05 | 24588402 | G | C | 99.60% | 0.00% | G -> C,A | NA |
LOC_Os05g42000.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os05g42010.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os05g42010.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os05g41990.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g42000.2 Alt: A| intron_variant MODIFIER(snpEff) LOC_Os05g42000.1 Alt: C| synonymous_variant LOW(snpEff) LOC_Os05g42010.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os05g42010.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os05g41990.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g42000.2 Alt: C| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 86.829; most accessible tissue: Zhenshan97 flower, score: 94.226 |
| vg0524588403 (J) | chr05 | 24588403 | G | T | 99.60% | 0.00% | G -> T | NA |
LOC_Os05g42000.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os05g42010.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os05g42010.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os05g41990.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g42000.2 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 86.814; most accessible tissue: Zhenshan97 flower, score: 94.209 |
| vg0524588473 (J) | chr05 | 24588473 | C | G | 55.70% | 0.08% | G -> C |
mr1032 (All); LR P-value: 3.83E-15;
mr1165 (All); LR P-value: 1.41E-15; mr1170 (Ind_All); LR P-value: 7.71E-06; mr1478 (All); LR P-value: 8.42E-15; mr1889 (All); LMM P-value: 1.17E-10; LR P-value: 1.50E-58; mr1889 (Ind_All); LMM P-value: 7.95E-17; LR P-value: 9.42E-31; mr1896 (All); LMM P-value: 1.71E-10; LR P-value: 9.05E-69; mr1896 (Ind_All); LMM P-value: 3.43E-16; LR P-value: 1.91E-29; mr1903 (All); LMM P-value: 3.57E-13; LR P-value: 3.82E-30; mr1903 (Ind_All); LMM P-value: 1.21E-17; LR P-value: 7.02E-31; mr1907 (All); LMM P-value: 5.63E-16; LR P-value: 7.36E-89; mr1907 (Ind_All); LMM P-value: 1.10E-23; LR P-value: 3.88E-47; mr1934 (All); LMM P-value: 1.48E-14; mr1934 (Ind_All); LMM P-value: 2.16E-19; LR P-value: 1.51E-36; mr1935 (All); LMM P-value: 9.80E-12; mr1935 (Ind_All); LMM P-value: 1.21E-15; LR P-value: 7.57E-28; mr1349_2 (All); LR P-value: 6.95E-10; mr1478_2 (All); LR P-value: 1.70E-08; mr1612_2 (All); LMM P-value: 4.15E-07; LR P-value: 1.35E-11; mr1715_2 (Ind_All); LR P-value: 1.10E-09; mr1889_2 (All); LMM P-value: 1.41E-07; LR P-value: 1.54E-68; mr1889_2 (Ind_All); LMM P-value: 1.35E-09; LR P-value: 7.60E-25; mr1896_2 (All); LMM P-value: 1.83E-09; LR P-value: 1.14E-66; mr1896_2 (Ind_All); LMM P-value: 3.00E-12; LR P-value: 3.94E-24; mr1907_2 (All); LMM P-value: 2.64E-12; LR P-value: 3.83E-94; mr1907_2 (Ind_All); LMM P-value: 8.32E-15; LR P-value: 3.81E-34; mr1934_2 (All); LMM P-value: 1.19E-11; mr1934_2 (Ind_All); LMM P-value: 3.99E-15; LR P-value: 2.64E-33 |
LOC_Os05g42000.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g42000.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 90.698; most accessible tissue: Zhenshan97 flower, score: 94.601 |
| vg0524588797 (J) | chr05 | 24588797 | GTT | G | 94.60% | 0.00% | GTT -> G | NA |
LOC_Os05g42000.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g42010.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g42000.2 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g42010.2 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41990.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 90.041; most accessible tissue: Zhenshan97 root, score: 96.450 |
| vg0524589166 (J) | chr05 | 24589166 | C | CT | 61.50% | 0.11% | CT -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g42000.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g42010.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g42000.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g42010.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41990.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.644; most accessible tissue: Zhenshan97 root, score: 94.490 |
| vg0524589229 (J) | chr05 | 24589229 | C | T | 98.50% | 0.00% | C -> T | NA |
LOC_Os05g42000.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g42010.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g42000.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g42010.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41990.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 69.709; most accessible tissue: Callus, score: 94.457 |
| STR0524587900 (J) | chr05 | 24587900 | GGCG | GGCA | 97.40% | 0.00% | GGCG -> GGCA | NA |
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