33 variations found. LOC_Os05g45400 (expressed protein), ranging from 26,333,792 bp to 26,337,324 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0526333978 (J) | chr05 | 26333978 | T | A | 99.50% | 0.00% | T -> A | NA |
LOC_Os05g45400.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os05g45390.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 78.852; most accessible tissue: Callus, score: 91.810 |
| vg0526334072 (J) | chr05 | 26334072 | G | A | 60.80% | 0.42% | A -> G |
mr1016 (All); LR P-value: 3.95E-46;
mr1016 (Ind_All); LR P-value: 7.42E-13; mr1022 (All); LR P-value: 1.48E-30; mr1022 (Ind_All); LR P-value: 2.90E-14; mr1044 (All); LR P-value: 4.08E-06; mr1059 (All); LR P-value: 1.88E-14; mr1079 (Ind_All); LR P-value: 1.60E-12; mr1142 (Ind_All); LR P-value: 1.91E-11; mr1178 (Ind_All); LR P-value: 1.11E-12; mr1301 (Ind_All); LR P-value: 6.07E-08; mr1390 (Ind_All); LR P-value: 2.45E-11; mr1490 (All); LR P-value: 6.05E-52; mr1490 (Ind_All); LR P-value: 3.69E-12; mr1491 (Ind_All); LR P-value: 2.10E-10; mr1546 (All); LR P-value: 1.68E-31; mr1546 (Ind_All); LR P-value: 4.12E-09; mr1599 (Ind_All); LR P-value: 6.23E-07; mr1726 (All); LR P-value: 8.14E-14; mr1915 (All); LR P-value: 1.57E-07; mr1022_2 (All); LR P-value: 4.10E-36; mr1030_2 (All); LR P-value: 1.48E-07; mr1093_2 (Ind_All); LR P-value: 8.69E-08; mr1109_2 (Ind_All); LR P-value: 1.19E-08; mr1132_2 (Ind_All); LR P-value: 1.04E-11; mr1141_2 (All); LR P-value: 5.26E-55; mr1175_2 (All); LR P-value: 1.54E-21; mr1193_2 (All); LR P-value: 2.73E-10; mr1193_2 (Ind_All); LR P-value: 8.42E-06; mr1195_2 (All); LR P-value: 5.34E-23; mr1195_2 (Ind_All); LR P-value: 1.97E-11; mr1235_2 (Ind_All); LR P-value: 2.39E-08; mr1349_2 (All); LR P-value: 9.62E-10; mr1352_2 (Ind_All); LR P-value: 1.71E-10; mr1358_2 (All); LR P-value: 5.16E-07; mr1408_2 (All); LR P-value: 3.91E-07; mr1482_2 (All); LR P-value: 3.39E-07; mr1482_2 (Ind_All); LR P-value: 2.51E-06; mr1546_2 (All); LR P-value: 6.11E-53; mr1546_2 (Ind_All); LR P-value: 1.45E-12; mr1587_2 (All); LR P-value: 5.32E-16; mr1592_2 (All); LR P-value: 1.81E-16; mr1599_2 (All); LR P-value: 6.92E-58; mr1599_2 (Ind_All); LR P-value: 7.88E-09; mr1645_2 (All); LR P-value: 5.71E-08; mr1654_2 (All); LR P-value: 3.13E-08; mr1654_2 (Ind_All); LR P-value: 6.00E-07; mr1682_2 (Ind_All); LR P-value: 1.79E-06; mr1780_2 (All); LR P-value: 2.03E-32; mr1790_2 (All); LR P-value: 2.73E-14; mr1805_2 (Ind_All); LR P-value: 1.08E-07; mr1828_2 (All); LMM P-value: 6.54E-07; LR P-value: 7.45E-73; mr1828_2 (Ind_All); LMM P-value: 1.90E-06; LR P-value: 1.87E-11; mr1837_2 (All); LR P-value: 5.63E-08; mr1893_2 (All); LR P-value: 2.46E-11; mr1915_2 (All); LR P-value: 9.21E-07; mr1938_2 (All); LR P-value: 3.18E-15 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g45400.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g45390.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 81.004; most accessible tissue: Callus, score: 91.810 |
| vg0526334129 (J) | chr05 | 26334129 | A | C | 60.80% | 0.38% | C -> A |
mr1016 (All); LR P-value: 4.33E-47;
mr1016 (Ind_All); LR P-value: 7.42E-13; mr1022 (All); LR P-value: 8.43E-31; mr1022 (Ind_All); LR P-value: 2.90E-14; mr1044 (All); LR P-value: 2.82E-06; mr1059 (All); LR P-value: 1.92E-14; mr1079 (Ind_All); LR P-value: 1.60E-12; mr1141 (All); LR P-value: 4.96E-43; mr1142 (Ind_All); LR P-value: 1.91E-11; mr1178 (Ind_All); LR P-value: 1.11E-12; mr1301 (Ind_All); LR P-value: 6.07E-08; mr1390 (All); LR P-value: 3.24E-53; mr1390 (Ind_All); LR P-value: 2.45E-11; mr1490 (All); LR P-value: 2.70E-53; mr1490 (Ind_All); LR P-value: 3.69E-12; mr1491 (Ind_All); LR P-value: 2.10E-10; mr1546 (All); LR P-value: 1.61E-32; mr1546 (Ind_All); LR P-value: 4.12E-09; mr1599 (Ind_All); LR P-value: 6.23E-07; mr1726 (All); LR P-value: 5.42E-14; mr1903 (All); LR P-value: 7.67E-25; mr1915 (All); LR P-value: 6.35E-08; mr1022_2 (All); LR P-value: 2.45E-36; mr1030_2 (All); LR P-value: 1.19E-07; mr1093_2 (Ind_All); LR P-value: 8.69E-08; mr1109_2 (Ind_All); LR P-value: 1.19E-08; mr1132_2 (Ind_All); LR P-value: 1.04E-11; mr1141_2 (All); LR P-value: 1.16E-55; mr1175_2 (All); LR P-value: 4.78E-21; mr1193_2 (Ind_All); LR P-value: 8.42E-06; mr1195_2 (All); LR P-value: 2.75E-23; mr1195_2 (Ind_All); LR P-value: 1.97E-11; mr1235_2 (All); LR P-value: 2.61E-52; mr1235_2 (Ind_All); LR P-value: 2.39E-08; mr1349_2 (All); LR P-value: 1.18E-09; mr1352_2 (Ind_All); LR P-value: 1.71E-10; mr1358_2 (All); LR P-value: 4.60E-07; mr1408_2 (All); LR P-value: 4.68E-07; mr1482_2 (All); LR P-value: 2.12E-07; mr1482_2 (Ind_All); LR P-value: 2.51E-06; mr1546_2 (All); LR P-value: 9.41E-54; mr1546_2 (Ind_All); LR P-value: 1.45E-12; mr1587_2 (All); LR P-value: 4.10E-16; mr1592_2 (All); LR P-value: 1.10E-16; mr1599_2 (All); LR P-value: 3.42E-60; mr1599_2 (Ind_All); LR P-value: 7.88E-09; mr1645_2 (All); LR P-value: 1.08E-07; mr1654_2 (All); LR P-value: 3.09E-08; mr1654_2 (Ind_All); LR P-value: 6.00E-07; mr1682_2 (Ind_All); LR P-value: 1.79E-06; mr1780_2 (All); LR P-value: 8.76E-33; mr1790_2 (All); LR P-value: 1.52E-14; mr1805_2 (Ind_All); LR P-value: 1.08E-07; mr1828_2 (All); LMM P-value: 2.45E-08; LR P-value: 7.90E-76; mr1828_2 (Ind_All); LMM P-value: 1.90E-06; LR P-value: 1.87E-11; mr1837_2 (All); LR P-value: 5.03E-08; mr1893_2 (All); LR P-value: 1.51E-11; mr1915_2 (All); LR P-value: 9.01E-07; mr1938_2 (All); LR P-value: 2.32E-15 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g45400.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g45390.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.439; most accessible tissue: Minghui63 flag leaf, score: 88.798 |
| vg0526334208 (J) | chr05 | 26334208 | A | G | 93.10% | 0.00% | A -> G | NA |
LOC_Os05g45400.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g45390.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.747; most accessible tissue: Callus, score: 90.045 |
| vg0526334385 (J) | chr05 | 26334385 | CG | C | 99.40% | 0.00% | CG -> C | NA |
LOC_Os05g45400.1 Alt: C| splice_region_variant&intron_variant LOW(snpEff)
LOC_Os05g45390.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 77.660; most accessible tissue: Minghui63 flag leaf, score: 89.425 |
| vg0526334584 (J) | chr05 | 26334584 | C | T | 92.10% | 0.00% | C -> T | NA |
LOC_Os05g45400.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 70.407; most accessible tissue: Minghui63 flag leaf, score: 84.227 |
| vg0526334812 (J) | chr05 | 26334812 | A | T | 60.80% | 0.02% | T -> A |
mr1016 (All); LR P-value: 1.11E-46;
mr1016 (Ind_All); LR P-value: 7.42E-13; mr1022 (All); LR P-value: 4.00E-30; mr1022 (Ind_All); LR P-value: 2.90E-14; mr1044 (All); LR P-value: 2.33E-06; mr1059 (All); LR P-value: 1.09E-14; mr1079 (Ind_All); LR P-value: 1.60E-12; mr1142 (Ind_All); LR P-value: 1.91E-11; mr1178 (Ind_All); LR P-value: 1.11E-12; mr1301 (Ind_All); LR P-value: 6.07E-08; mr1390 (All); LR P-value: 3.53E-52; mr1390 (Ind_All); LR P-value: 2.45E-11; mr1490 (All); LR P-value: 2.34E-52; mr1490 (Ind_All); LR P-value: 3.69E-12; mr1491 (Ind_All); LR P-value: 2.10E-10; mr1535 (All); LR P-value: 1.69E-14; mr1546 (All); LR P-value: 7.45E-32; mr1546 (Ind_All); LR P-value: 4.12E-09; mr1599 (Ind_All); LR P-value: 6.23E-07; mr1675 (All); LR P-value: 7.54E-15; mr1726 (All); LR P-value: 4.98E-14; mr1915 (All); LR P-value: 2.29E-07; mr1969 (All); LR P-value: 2.63E-14; mr1030_2 (All); LR P-value: 1.52E-07; mr1093_2 (Ind_All); LR P-value: 8.69E-08; mr1109_2 (Ind_All); LR P-value: 1.19E-08; mr1132_2 (Ind_All); LR P-value: 1.04E-11; mr1141_2 (All); LR P-value: 2.76E-54; mr1175_2 (All); LR P-value: 3.18E-21; mr1193_2 (All); LR P-value: 2.32E-10; mr1193_2 (Ind_All); LR P-value: 8.42E-06; mr1195_2 (All); LR P-value: 7.78E-23; mr1195_2 (Ind_All); LR P-value: 1.97E-11; mr1235_2 (Ind_All); LR P-value: 2.39E-08; mr1352_2 (Ind_All); LR P-value: 1.71E-10; mr1358_2 (All); LR P-value: 3.03E-07; mr1478_2 (All); LR P-value: 1.61E-08; mr1482_2 (All); LR P-value: 1.27E-07; mr1482_2 (Ind_All); LR P-value: 2.51E-06; mr1520_2 (All); LR P-value: 2.22E-11; mr1546_2 (All); LR P-value: 2.56E-53; mr1546_2 (Ind_All); LR P-value: 1.45E-12; mr1587_2 (All); LR P-value: 1.79E-15; mr1592_2 (All); LR P-value: 1.20E-16; mr1599_2 (Ind_All); LR P-value: 7.88E-09; mr1645_2 (All); LR P-value: 6.78E-08; mr1654_2 (All); LR P-value: 9.62E-08; mr1654_2 (Ind_All); LR P-value: 6.00E-07; mr1682_2 (Ind_All); LR P-value: 1.79E-06; mr1780_2 (All); LR P-value: 2.21E-32; mr1805_2 (Ind_All); LR P-value: 1.08E-07; mr1828_2 (All); LMM P-value: 6.13E-07; LR P-value: 1.08E-72; mr1828_2 (Ind_All); LMM P-value: 1.90E-06; LR P-value: 1.87E-11; mr1837_2 (All); LR P-value: 4.18E-08; mr1893_2 (All); LR P-value: 5.25E-11; mr1915_2 (All); LR P-value: 1.05E-06; mr1938_2 (All); LR P-value: 5.96E-15 |
LOC_Os05g45400.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g45400.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 67.865; most accessible tissue: Callus, score: 84.657 |
| vg0526335029 (J) | chr05 | 26335029 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os05g45400.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os05g45390.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 56.626; most accessible tissue: Callus, score: 83.184 |
| vg0526335065 (J) | chr05 | 26335065 | T | C | 99.80% | 0.00% | T -> C | NA |
LOC_Os05g45400.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 52.527; most accessible tissue: Callus, score: 83.184 |
| vg0526335102 (J) | chr05 | 26335102 | C | T | 62.70% | 0.19% | T -> C |
mr1016 (All); LR P-value: 2.33E-45;
mr1016 (Ind_All); LR P-value: 6.76E-13; mr1022 (All); LR P-value: 3.57E-30; mr1022 (Ind_All); LR P-value: 4.72E-14; mr1044 (Ind_All); LR P-value: 4.08E-06; mr1059 (All); LR P-value: 1.06E-16; mr1079 (Ind_All); LR P-value: 2.76E-12; mr1105 (All); LR P-value: 2.46E-36; mr1141 (All); LR P-value: 3.49E-43; mr1142 (Ind_All); LR P-value: 8.07E-11; mr1143 (All); LR P-value: 1.25E-16; mr1167 (All); LR P-value: 2.15E-17; mr1178 (All); LR P-value: 1.45E-54; mr1178 (Ind_All); LR P-value: 2.42E-12; mr1301 (Ind_All); LR P-value: 6.33E-08; mr1489 (Ind_All); LR P-value: 9.60E-07; mr1490 (All); LR P-value: 2.26E-51; mr1490 (Ind_All); LR P-value: 2.18E-11; mr1491 (Ind_All); LR P-value: 4.10E-10; mr1535 (All); LR P-value: 6.58E-16; mr1546 (All); LR P-value: 3.31E-29; mr1546 (Ind_All); LR P-value: 7.75E-09; mr1675 (All); LR P-value: 1.07E-16; mr1726 (All); LR P-value: 4.84E-15; mr1903 (All); LR P-value: 1.41E-25; mr1915 (All); LR P-value: 7.00E-07; mr1934 (All); LR P-value: 1.44E-74; mr1935 (All); LR P-value: 1.69E-51; mr1950 (All); LR P-value: 1.61E-15; mr1969 (All); LR P-value: 3.30E-16; mr1995 (All); LR P-value: 6.79E-18; mr1105_2 (All); LR P-value: 2.16E-30; mr1115_2 (Ind_All); LR P-value: 2.61E-06; mr1141_2 (All); LR P-value: 6.66E-56; mr1167_2 (All); LR P-value: 1.21E-19; mr1175_2 (All); LR P-value: 4.96E-22; mr1193_2 (Ind_All); LR P-value: 2.19E-06; mr1195_2 (All); LR P-value: 7.86E-23; mr1195_2 (Ind_All); LR P-value: 4.47E-12; mr1352_2 (Ind_All); LR P-value: 1.61E-10; mr1358_2 (All); LR P-value: 9.48E-07; mr1408_2 (All); LR P-value: 4.83E-07; mr1416_2 (All); LR P-value: 8.29E-16; mr1482_2 (Ind_All); LR P-value: 2.28E-06; mr1546_2 (All); LR P-value: 2.46E-52; mr1546_2 (Ind_All); LR P-value: 3.17E-12; mr1580_2 (Ind_All); LR P-value: 6.18E-06; mr1599_2 (Ind_All); LR P-value: 5.38E-08; mr1645_2 (All); LR P-value: 2.36E-08; mr1645_2 (Ind_All); LR P-value: 8.13E-06; mr1654_2 (All); LR P-value: 2.10E-07; mr1682_2 (Ind_All); LR P-value: 9.73E-08; mr1805_2 (Ind_All); LR P-value: 3.21E-07; mr1821_2 (All); LR P-value: 2.27E-07; mr1825_2 (Ind_All); LR P-value: 8.41E-06; mr1828_2 (All); LMM P-value: 5.08E-09; LR P-value: 1.18E-79; mr1828_2 (Ind_All); LMM P-value: 2.11E-07; LR P-value: 6.07E-13; mr1837_2 (All); LR P-value: 2.49E-07; mr1893_2 (All); LR P-value: 6.04E-11; mr1907_2 (Ind_All); LR P-value: 2.51E-08; mr1915_2 (All); LR P-value: 3.46E-06; mr1938_2 (All); LR P-value: 4.03E-15; mr1938_2 (Ind_All); LR P-value: 7.35E-06 |
LOC_Os05g45400.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g45400.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 49.648; most accessible tissue: Minghui63 flag leaf, score: 64.284 |
| vg0526335149 (J) | chr05 | 26335149 | AAT | A | 62.60% | 0.28% | A -> AAT | NA |
LOC_Os05g45390.1 Alt: AAT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g45400.1 Alt: AAT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 49.568; most accessible tissue: Minghui63 flag leaf, score: 68.675 |
| vg0526335257 (J) | chr05 | 26335257 | C | T | 99.70% | 0.00% | C -> T | NA |
LOC_Os05g45390.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os05g45400.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 46.626; most accessible tissue: Callus, score: 82.662 |
| vg0526335394 (J) | chr05 | 26335394 | G | A | 99.50% | 0.00% | G -> A | NA |
LOC_Os05g45390.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os05g45400.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 49.017; most accessible tissue: Minghui63 flag leaf, score: 68.160 |
| vg0526335632 (J) | chr05 | 26335632 | A | G | 99.90% | 0.00% | A -> G | NA |
LOC_Os05g45390.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os05g45400.1 Alt: G| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 53.391; most accessible tissue: Minghui63 flag leaf, score: 68.675 |
| vg0526335924 (J) | chr05 | 26335924 | G | T | 99.50% | 0.00% | G -> T | NA |
LOC_Os05g45400.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os05g45390.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 53.632; most accessible tissue: Zhenshan97 flag leaf, score: 69.147 |
| vg0526335948 (J) | chr05 | 26335948 | C | T | 98.80% | 0.00% | C -> T | NA |
LOC_Os05g45400.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 57.780; most accessible tissue: Callus, score: 79.709 |
| vg0526336095 (J) | chr05 | 26336095 | G | A | 60.90% | 0.06% | A -> G |
mr1016 (All); LR P-value: 2.86E-46;
mr1016 (Ind_All); LR P-value: 7.42E-13; mr1022 (All); LR P-value: 3.35E-30; mr1022 (Ind_All); LR P-value: 2.90E-14; mr1044 (All); LR P-value: 3.67E-06; mr1059 (All); LR P-value: 1.35E-14; mr1079 (Ind_All); LR P-value: 1.60E-12; mr1142 (Ind_All); LR P-value: 1.91E-11; mr1149 (All); LR P-value: 1.34E-12; mr1178 (Ind_All); LR P-value: 1.11E-12; mr1301 (Ind_All); LR P-value: 6.07E-08; mr1390 (Ind_All); LR P-value: 2.45E-11; mr1490 (All); LR P-value: 3.02E-52; mr1490 (Ind_All); LR P-value: 3.69E-12; mr1491 (Ind_All); LR P-value: 2.10E-10; mr1546 (All); LR P-value: 8.44E-32; mr1546 (Ind_All); LR P-value: 4.12E-09; mr1599 (Ind_All); LR P-value: 6.23E-07; mr1675 (All); LR P-value: 1.12E-14; mr1726 (All); LR P-value: 5.80E-14; mr1915 (All); LR P-value: 1.22E-07; mr1030_2 (All); LR P-value: 1.50E-07; mr1093_2 (Ind_All); LR P-value: 8.69E-08; mr1109_2 (Ind_All); LR P-value: 1.19E-08; mr1132_2 (Ind_All); LR P-value: 1.04E-11; mr1141_2 (All); LR P-value: 3.56E-55; mr1175_2 (All); LR P-value: 4.24E-21; mr1193_2 (All); LR P-value: 1.77E-10; mr1193_2 (Ind_All); LR P-value: 8.42E-06; mr1195_2 (All); LR P-value: 4.32E-23; mr1195_2 (Ind_All); LR P-value: 1.97E-11; mr1235_2 (Ind_All); LR P-value: 2.39E-08; mr1352_2 (Ind_All); LR P-value: 1.71E-10; mr1358_2 (All); LR P-value: 4.16E-07; mr1408_2 (All); LR P-value: 4.72E-07; mr1482_2 (All); LR P-value: 2.24E-07; mr1482_2 (Ind_All); LR P-value: 2.51E-06; mr1546_2 (All); LR P-value: 5.52E-53; mr1546_2 (Ind_All); LR P-value: 1.45E-12; mr1587_2 (All); LR P-value: 5.35E-16; mr1592_2 (All); LR P-value: 6.56E-17; mr1599_2 (All); LR P-value: 1.40E-58; mr1599_2 (Ind_All); LR P-value: 7.88E-09; mr1645_2 (All); LR P-value: 6.48E-08; mr1654_2 (All); LR P-value: 3.65E-08; mr1654_2 (Ind_All); LR P-value: 6.00E-07; mr1682_2 (Ind_All); LR P-value: 1.79E-06; mr1780_2 (All); LR P-value: 2.26E-32; mr1790_2 (All); LR P-value: 2.47E-14; mr1805_2 (Ind_All); LR P-value: 1.08E-07; mr1828_2 (All); LMM P-value: 2.21E-07; LR P-value: 7.00E-74; mr1828_2 (Ind_All); LMM P-value: 1.90E-06; LR P-value: 1.87E-11; mr1837_2 (All); LR P-value: 5.06E-08; mr1893_2 (All); LR P-value: 1.99E-11; mr1915_2 (All); LR P-value: 9.40E-07; mr1938_2 (All); LR P-value: 2.99E-15 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g45390.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g45400.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 56.418; most accessible tissue: Minghui63 young leaf, score: 68.070 |
| vg0526336130 (J) | chr05 | 26336130 | A | C | 79.70% | 4.89% | A -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g45390.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g45400.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 59.241; most accessible tissue: Zhenshan97 flag leaf, score: 71.238 |
| vg0526336258 (J) | chr05 | 26336258 | C | A | 99.40% | 0.00% | C -> A | NA |
LOC_Os05g45390.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os05g45400.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 61.799; most accessible tissue: Callus, score: 86.382 |
| vg0526336481 (J) | chr05 | 26336481 | T | C | 99.40% | 0.00% | T -> C | NA |
LOC_Os05g45400.1 Alt: C| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 74.392; most accessible tissue: Minghui63 flag leaf, score: 92.302 |
| vg0526336610 (J) | chr05 | 26336610 | C | G | 99.50% | 0.00% | C -> G | NA |
LOC_Os05g45400.1 Alt: G| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 83.004; most accessible tissue: Minghui63 flag leaf, score: 94.939 |
| vg0526336735 (J) | chr05 | 26336735 | ACCTCCC | A | 99.40% | 0.00% | ACCTCCC -> A | NA |
LOC_Os05g45400.1 Alt: A| disruptive_inframe_deletion MODERATE(snpEff)
The average chromatin accessibility score: 89.279; most accessible tissue: Minghui63 flag leaf, score: 96.383 |
| vg0526336743 (J) | chr05 | 26336743 | C | CGGG | 99.40% | 0.00% | C -> CGGG | NA |
The average chromatin accessibility score: 89.425; most accessible tissue: Minghui63 flag leaf, score: 96.451
|
| vg0526336770 (J) | chr05 | 26336770 | C | A | 99.50% | 0.00% | C -> A | NA |
LOC_Os05g45400.1 Alt: A| synonymous_variant LOW(snpEff)
The average chromatin accessibility score: 90.755; most accessible tissue: Minghui63 flag leaf, score: 97.125 |
| vg0526336814 (J) | chr05 | 26336814 | G | C | 98.90% | 0.00% | G -> C | NA |
LOC_Os05g45400.1 Alt: C| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 92.398; most accessible tissue: Minghui63 flag leaf, score: 97.719 |
| vg0526336840 (J) | chr05 | 26336840 | A | G | 99.40% | 0.00% | A -> G | NA |
LOC_Os05g45400.1 Alt: G| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 89.830; most accessible tissue: Minghui63 flag leaf, score: 97.812 |
| vg0526336905 (J) | chr05 | 26336905 | G | A | 98.90% | 0.00% | G -> A | NA |
LOC_Os05g45400.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 91.226; most accessible tissue: Zhenshan97 flag leaf, score: 98.467 |
| vg0526337022 (J) | chr05 | 26337022 | G | T | 99.40% | 0.00% | G -> T | NA |
LOC_Os05g45400.1 Alt: T| synonymous_variant LOW(snpEff)
The average chromatin accessibility score: 96.473; most accessible tissue: Zhenshan97 flag leaf, score: 99.098 |
| vg0526337083 (J) | chr05 | 26337083 | T | G | 68.70% | 9.84% | T -> G | NA |
LOC_Os05g45400.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g45400.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 96.066; most accessible tissue: Zhenshan97 flag leaf, score: 99.247 |
| vg0526337085 (J) | chr05 | 26337085 | C | G | 75.30% | 7.49% | C -> G | NA |
LOC_Os05g45400.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g45400.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 96.187; most accessible tissue: Zhenshan97 flag leaf, score: 99.289 |
| vg0526337186 (J) | chr05 | 26337186 | C | T | 62.70% | 0.00% | T -> C |
mr1016 (All); LR P-value: 2.26E-46;
mr1016 (Ind_All); LR P-value: 3.48E-14; mr1022 (All); LR P-value: 3.32E-31; mr1022 (Ind_All); LR P-value: 1.72E-15; mr1044 (Ind_All); LR P-value: 1.90E-06; mr1059 (All); LR P-value: 1.23E-16; mr1079 (Ind_All); LR P-value: 7.73E-14; mr1105 (All); LR P-value: 6.59E-35; mr1142 (Ind_All); LR P-value: 3.62E-12; mr1143 (All); LR P-value: 2.59E-16; mr1167 (All); LR P-value: 4.94E-17; mr1178 (All); LR P-value: 2.71E-55; mr1178 (Ind_All); LR P-value: 1.00E-13; mr1301 (Ind_All); LR P-value: 2.33E-08; mr1352 (Ind_All); LR P-value: 5.60E-06; mr1390 (Ind_All); LR P-value: 4.40E-12; mr1489 (Ind_All); LR P-value: 4.09E-07; mr1490 (All); LR P-value: 1.14E-51; mr1490 (Ind_All); LR P-value: 7.48E-13; mr1491 (Ind_All); LR P-value: 2.94E-11; mr1535 (All); LR P-value: 8.77E-16; mr1546 (All); LR P-value: 3.64E-30; mr1546 (Ind_All); LR P-value: 2.51E-10; mr1675 (All); LR P-value: 2.72E-16; mr1677 (All); LR P-value: 2.63E-06; mr1726 (All); LR P-value: 5.27E-15; mr1903 (All); LR P-value: 1.02E-24; mr1915 (All); LR P-value: 1.81E-07; mr1934 (All); LR P-value: 1.59E-74; mr1950 (All); LR P-value: 1.35E-15; mr1969 (All); LR P-value: 9.65E-16; mr1995 (All); LR P-value: 9.37E-18; mr1022_2 (Ind_All); LR P-value: 9.87E-14; mr1030_2 (All); LR P-value: 3.03E-07; mr1079_2 (Ind_All); LR P-value: 1.67E-12; mr1115_2 (Ind_All); LR P-value: 1.38E-06; mr1132_2 (Ind_All); LR P-value: 2.18E-12; mr1141_2 (All); LR P-value: 3.31E-56; mr1167_2 (All); LR P-value: 7.82E-19; mr1175_2 (All); LR P-value: 3.91E-22; mr1178_2 (Ind_All); LR P-value: 8.05E-13; mr1193_2 (Ind_All); LR P-value: 1.91E-06; mr1195_2 (All); LR P-value: 9.15E-23; mr1195_2 (Ind_All); LR P-value: 3.04E-12; mr1235_2 (Ind_All); LR P-value: 7.63E-08; mr1241_2 (Ind_All); LR P-value: 3.55E-08; mr1253_2 (Ind_All); LR P-value: 8.37E-06; mr1277_2 (All); LR P-value: 1.89E-14; mr1352_2 (Ind_All); LR P-value: 7.22E-11; mr1358_2 (All); LR P-value: 8.61E-07; mr1390_2 (Ind_All); LR P-value: 9.92E-13; mr1403_2 (All); LR P-value: 1.28E-23; mr1408_2 (All); LR P-value: 1.51E-07; mr1482_2 (Ind_All); LR P-value: 5.66E-07; mr1489_2 (Ind_All); LR P-value: 9.27E-08; mr1490_2 (Ind_All); LR P-value: 5.40E-12; mr1546_2 (All); LR P-value: 3.38E-53; mr1546_2 (Ind_All); LR P-value: 8.01E-14; mr1580_2 (Ind_All); LR P-value: 1.37E-06; mr1587_2 (All); LR P-value: 1.00E-15; mr1599_2 (All); LR P-value: 3.87E-59; mr1599_2 (Ind_All); LR P-value: 1.50E-08; mr1645_2 (All); LR P-value: 8.40E-08; mr1654_2 (All); LR P-value: 3.17E-07; mr1654_2 (Ind_All); LR P-value: 6.54E-06; mr1682_2 (Ind_All); LR P-value: 1.89E-07; mr1780_2 (All); LR P-value: 7.19E-33; mr1805_2 (Ind_All); LR P-value: 4.40E-08; mr1825_2 (Ind_All); LR P-value: 2.23E-06; mr1828_2 (All); LMM P-value: 3.20E-09; LR P-value: 2.82E-79; mr1828_2 (Ind_All); LMM P-value: 2.15E-07; LR P-value: 1.00E-12; mr1837_2 (All); LR P-value: 9.43E-08; mr1915_2 (All); LR P-value: 5.37E-07; mr1938_2 (All); LR P-value: 1.65E-15; mr1938_2 (Ind_All); LR P-value: 5.36E-06 |
LOC_Os05g45400.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 99.215; most accessible tissue: Zhenshan97 flag leaf, score: 99.655 |
| vg0526337215 (J) | chr05 | 26337215 | A | AGCG | 99.60% | 0.00% | A -> AGCG | NA |
The average chromatin accessibility score: 99.337; most accessible tissue: Zhenshan97 flag leaf, score: 99.694
|
| vg0526337294 (J) | chr05 | 26337294 | T | TGGA | 61.10% | 0.00% | TGGA -> T | NA |
LOC_Os05g45400.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 99.624; most accessible tissue: Minghui63 panicle, score: 99.811 |