18 variations found. LOC_Os01g56690 (helix-loop-helix DNA-binding domain containing protein; expressed), ranging from 32,714,778 bp to 32,716,417 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0132714853 (J) | chr01 | 32714853 | C | A | 78.10% | 0.00% | C -> A |
mr1156_2 (Ind_All); LR P-value: 8.74E-06;
mr1167_2 (Ind_All); LR P-value: 7.74E-07; mr1193_2 (Ind_All); LR P-value: 6.50E-07; mr1321_2 (All); LR P-value: 3.18E-07; mr1478_2 (All); LR P-value: 8.04E-09; mr1641_2 (Ind_All); LR P-value: 3.01E-07; mr1654_2 (All); LR P-value: 6.60E-07; mr1759_2 (Ind_All); LR P-value: 8.11E-06; mr1794_2 (Ind_All); LR P-value: 3.69E-12 |
LOC_Os01g56690.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 96.600; most accessible tissue: Zhenshan97 flag leaf, score: 99.696 |
| vg0132714901 (J) | chr01 | 32714901 | T | TCCGCCG | 83.20% | 0.00% | T -> TCCGCCG | NA |
The average chromatin accessibility score: 95.826; most accessible tissue: Zhenshan97 flag leaf, score: 99.555
|
| vg0132714966 (J) | chr01 | 32714966 | C | T | 96.60% | 0.00% | C -> T | NA |
LOC_Os01g56690.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 95.465; most accessible tissue: Zhenshan97 flag leaf, score: 99.349 |
| vg0132715049 (J) | chr01 | 32715049 | C | T | 88.70% | 0.00% | C -> T |
mr1090 (Jap_All); LR P-value: 1.31E-06;
mr1097 (All); LR P-value: 5.83E-10; mr1206 (All); LR P-value: 1.03E-06; mr1241 (Jap_All); LR P-value: 1.33E-11; mr1248 (All); LR P-value: 1.25E-06; mr1338 (All); LR P-value: 7.28E-07; mr1425 (All); LR P-value: 1.25E-06; mr1449 (All); LR P-value: 2.98E-14; mr1449 (Jap_All); LR P-value: 1.93E-08; mr1539 (All); LR P-value: 2.91E-10; mr1540 (All); LR P-value: 8.88E-13; mr1540 (Jap_All); LR P-value: 1.45E-14; mr1642 (All); LR P-value: 5.14E-08; mr1671 (Jap_All); LR P-value: 4.24E-07; mr1699 (All); LR P-value: 1.13E-28; mr1732 (All); LR P-value: 1.62E-14; mr1732 (Jap_All); LR P-value: 2.23E-16; mr1742 (All); LR P-value: 2.27E-06; mr1742 (Jap_All); LR P-value: 2.25E-06; mr1870 (Jap_All); LR P-value: 5.17E-07; mr1871 (All); LR P-value: 8.69E-13; mr1880 (All); LR P-value: 4.08E-07; mr1089_2 (Jap_All); LR P-value: 6.08E-10; mr1090_2 (Jap_All); LR P-value: 1.75E-08; mr1092_2 (Jap_All); LR P-value: 8.75E-06; mr1097_2 (All); LR P-value: 1.31E-13; mr1097_2 (Jap_All); LR P-value: 1.20E-07; mr1121_2 (Jap_All); LR P-value: 1.23E-06; mr1206_2 (All); LR P-value: 1.98E-06; mr1211_2 (Jap_All); LR P-value: 4.09E-06; mr1295_2 (All); LR P-value: 8.91E-06; mr1319_2 (All); LR P-value: 1.47E-08; mr1319_2 (Jap_All); LR P-value: 2.18E-06; mr1334_2 (Jap_All); LR P-value: 1.36E-15; mr1363_2 (All); LR P-value: 2.50E-07; mr1425_2 (All); LR P-value: 2.50E-06; mr1471_2 (Jap_All); LR P-value: 7.80E-11; mr1502_2 (All); LR P-value: 3.08E-08; mr1526_2 (Jap_All); LR P-value: 8.76E-09; mr1539_2 (Jap_All); LR P-value: 1.04E-17; mr1540_2 (Jap_All); LR P-value: 8.05E-18; mr1543_2 (All); LR P-value: 3.38E-10; mr1574_2 (All); LR P-value: 8.42E-06; mr1642_2 (All); LR P-value: 5.82E-08; mr1642_2 (Jap_All); LR P-value: 5.68E-09; mr1668_2 (All); LR P-value: 4.15E-07; mr1671_2 (Jap_All); LR P-value: 2.92E-07; mr1679_2 (Jap_All); LR P-value: 5.67E-07; mr1680_2 (All); LR P-value: 2.63E-10; mr1696_2 (All); LR P-value: 4.80E-07; mr1699_2 (All); LR P-value: 1.00E-29; mr1699_2 (Jap_All); LR P-value: 4.70E-17; mr1732_2 (Jap_All); LR P-value: 4.17E-16; mr1742_2 (All); LR P-value: 5.91E-18; mr1742_2 (Jap_All); LR P-value: 4.55E-09; mr1771_2 (Jap_All); LR P-value: 6.89E-10; mr1781_2 (Jap_All); LR P-value: 3.08E-06; mr1784_2 (Jap_All); LR P-value: 2.72E-11; mr1786_2 (All); LR P-value: 3.09E-07; mr1789_2 (Jap_All); LR P-value: 6.13E-11; mr1798_2 (Jap_All); LR P-value: 3.86E-07; mr1817_2 (Jap_All); LR P-value: 2.49E-08; mr1862_2 (Jap_All); LR P-value: 1.42E-09; mr1871_2 (All); LR P-value: 3.24E-21; mr1966_2 (All); LR P-value: 5.48E-07 |
LOC_Os01g56690.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 94.080; most accessible tissue: Zhenshan97 flag leaf, score: 98.843 |
| vg0132715138 (J) | chr01 | 32715138 | G | A | 79.50% | 0.00% | G -> A |
Plant_height (All); LR P-value: 3.70E-23;
Plant_height (Ind_All); LR P-value: 1.58E-20; mr1011 (All); LR P-value: 7.27E-08; mr1011 (Ind_All); LR P-value: 3.32E-06; mr1014 (Ind_All); LR P-value: 3.78E-07; mr1015 (Ind_All); LR P-value: 1.05E-07; mr1021 (Ind_All); LR P-value: 6.44E-06; mr1031 (All); LR P-value: 8.49E-14; mr1031 (Ind_All); LR P-value: 2.23E-07; mr1032 (Ind_All); LR P-value: 1.60E-06; mr1056 (All); LR P-value: 3.65E-14; mr1056 (Ind_All); LR P-value: 1.86E-07; mr1059 (Ind_All); LR P-value: 1.02E-07; mr1352 (All); LR P-value: 1.36E-09; mr1477 (Ind_All); LR P-value: 1.29E-06; mr1478 (Ind_All); LR P-value: 8.55E-07; mr1675 (Ind_All); LR P-value: 1.68E-09; mr1794 (All); LR P-value: 2.33E-09; mr1950 (Ind_All); LR P-value: 4.97E-07; mr1971 (Ind_All); LR P-value: 6.72E-07; mr1060_2 (All); LR P-value: 1.96E-06; mr1060_2 (Ind_All); LR P-value: 4.30E-10; mr1064_2 (Ind_All); LR P-value: 1.16E-06; mr1156_2 (Ind_All); LR P-value: 4.27E-06; mr1172_2 (All); LR P-value: 3.27E-11; mr1186_2 (All); LR P-value: 4.45E-06; mr1186_2 (Ind_All); LR P-value: 8.09E-06; mr1268_2 (All); LR P-value: 2.14E-06; mr1268_2 (Ind_All); LR P-value: 1.71E-08; mr1319_2 (All); LR P-value: 1.11E-11; mr1319_2 (Ind_All); LR P-value: 1.27E-06; mr1327_2 (All); LR P-value: 7.75E-10; mr1327_2 (Ind_All); LR P-value: 1.23E-09; mr1330_2 (All); LR P-value: 6.11E-14; mr1330_2 (Ind_All); LR P-value: 4.11E-07; mr1332_2 (Ind_All); LR P-value: 7.61E-06; mr1346_2 (All); LR P-value: 8.72E-07; mr1352_2 (All); LR P-value: 4.74E-25; mr1352_2 (Ind_All); LR P-value: 2.52E-12; mr1358_2 (Ind_All); LR P-value: 6.04E-06; mr1359_2 (All); LR P-value: 8.98E-06; mr1359_2 (Ind_All); LR P-value: 7.22E-08; mr1360_2 (All); LR P-value: 9.83E-06; mr1378_2 (Ind_All); LR P-value: 3.07E-07; mr1428_2 (All); LR P-value: 1.55E-08; mr1428_2 (Ind_All); LR P-value: 1.89E-07; mr1439_2 (All); LR P-value: 2.55E-07; mr1454_2 (All); LR P-value: 8.52E-15; mr1454_2 (Ind_All); LR P-value: 5.59E-06; mr1478_2 (Ind_All); LR P-value: 1.39E-08; mr1579_2 (Ind_All); LR P-value: 7.75E-06; mr1624_2 (Ind_All); LR P-value: 2.75E-07; mr1653_2 (Ind_All); LR P-value: 9.22E-08; mr1850_2 (All); LR P-value: 4.18E-12; mr1971_2 (Ind_All); LR P-value: 2.11E-07; mr1994_2 (Ind_All); LR P-value: 5.39E-06 |
LOC_Os01g56690.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 89.119; most accessible tissue: Zhenshan97 flag leaf, score: 98.396 |
| vg0132715144 (J) | chr01 | 32715144 | G | A | 98.50% | 0.00% | G -> A | NA |
LOC_Os01g56690.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 89.080; most accessible tissue: Zhenshan97 flag leaf, score: 98.390 |
| vg0132715153 (J) | chr01 | 32715153 | C | T | 99.60% | 0.00% | C -> T | NA |
LOC_Os01g56690.1 Alt: T| synonymous_variant LOW(snpEff)
The average chromatin accessibility score: 88.858; most accessible tissue: Zhenshan97 flag leaf, score: 98.357 |
| vg0132715257 (J) | chr01 | 32715257 | C | T | 78.10% | 0.00% | C -> T |
mr1839 (Ind_All); LR P-value: 5.00E-06;
mr1156_2 (Ind_All); LR P-value: 3.55E-06; mr1193_2 (Ind_All); LR P-value: 8.30E-07; mr1321_2 (All); LR P-value: 2.33E-07; mr1478_2 (All); LR P-value: 9.98E-09; mr1641_2 (Ind_All); LR P-value: 8.73E-08; mr1654_2 (All); LR P-value: 7.17E-07; mr1706_2 (Ind_All); LR P-value: 9.38E-06; mr1756_2 (Ind_All); LR P-value: 1.98E-06; mr1759_2 (Ind_All); LR P-value: 6.16E-06; mr1794_2 (Ind_All); LR P-value: 3.43E-12 |
LOC_Os01g56690.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 89.936; most accessible tissue: Zhenshan97 flag leaf, score: 97.721 |
| vg0132715288 (J) | chr01 | 32715288 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os01g56690.1 Alt: A| synonymous_variant LOW(snpEff)
The average chromatin accessibility score: 89.429; most accessible tissue: Zhenshan97 flag leaf, score: 97.531 |
| vg0132715305 (J) | chr01 | 32715305 | A | G | 74.80% | 0.00% | G -> A |
mr1090 (Jap_All); LR P-value: 2.12E-06;
mr1217 (All); LR P-value: 3.65E-21; mr1241 (Jap_All); LR P-value: 7.97E-12; mr1300 (All); LR P-value: 6.17E-22; mr1334 (Jap_All); LR P-value: 5.18E-14; mr1364 (All); LR P-value: 2.93E-07; mr1401 (All); LR P-value: 5.05E-16; mr1410 (All); LR P-value: 1.25E-13; mr1422 (Jap_All); LR P-value: 1.84E-06; mr1449 (Jap_All); LR P-value: 1.04E-08; mr1471 (Jap_All); LR P-value: 1.54E-06; mr1539 (Jap_All); LR P-value: 1.97E-10; mr1540 (Jap_All); LR P-value: 8.63E-15; mr1563 (All); LR P-value: 4.23E-44; mr1642 (Jap_All); LR P-value: 2.09E-06; mr1671 (Jap_All); LR P-value: 1.58E-06; mr1679 (All); LR P-value: 7.33E-21; mr1732 (Jap_All); LR P-value: 4.84E-17; mr1740 (All); LR P-value: 4.73E-13; mr1742 (Jap_All); LR P-value: 2.52E-07; mr1771 (All); LR P-value: 9.40E-45; mr1784 (All); LR P-value: 1.14E-35; mr1845 (All); LR P-value: 5.21E-20; mr1870 (Jap_All); LR P-value: 3.09E-07; mr1926 (All); LR P-value: 8.26E-40; mr1077_2 (All); LR P-value: 3.36E-23; mr1089_2 (Jap_All); LR P-value: 4.41E-10; mr1090_2 (Jap_All); LR P-value: 3.86E-08; mr1097_2 (Jap_All); LR P-value: 2.43E-07; mr1121_2 (Jap_All); LR P-value: 9.13E-07; mr1211_2 (Jap_All); LR P-value: 6.52E-06; mr1235_2 (Jap_All); LR P-value: 5.29E-09; mr1241_2 (All); LR P-value: 2.32E-59; mr1250_2 (Jap_All); LR P-value: 8.13E-07; mr1304_2 (All); LR P-value: 3.54E-23; mr1319_2 (Jap_All); LR P-value: 6.45E-06; mr1334_2 (Jap_All); LR P-value: 8.01E-17; mr1425_2 (Jap_All); LR P-value: 6.57E-06; mr1471_2 (Jap_All); LR P-value: 8.74E-12; mr1526_2 (Jap_All); LR P-value: 1.49E-08; mr1539_2 (All); LR P-value: 2.77E-18; mr1539_2 (Jap_All); LR P-value: 3.80E-17; mr1540_2 (Jap_All); LR P-value: 2.94E-17; mr1642_2 (Jap_All); LR P-value: 6.93E-10; mr1679_2 (All); LR P-value: 1.10E-24; mr1679_2 (Jap_All); LR P-value: 3.58E-07; mr1699_2 (Jap_All); LR P-value: 3.81E-18; mr1732_2 (Jap_All); LR P-value: 7.85E-16; mr1742_2 (Jap_All); LR P-value: 2.60E-09; mr1771_2 (All); LR P-value: 1.18E-42; mr1781_2 (Jap_All); LR P-value: 3.10E-06; mr1784_2 (All); LR P-value: 2.41E-45; mr1784_2 (Jap_All); LR P-value: 5.33E-11; mr1789_2 (All); LR P-value: 2.74E-29; mr1789_2 (Jap_All); LR P-value: 1.16E-11; mr1798_2 (Jap_All); LR P-value: 2.98E-07; mr1808_2 (Jap_All); LR P-value: 9.18E-08; mr1817_2 (Jap_All); LR P-value: 2.34E-08; mr1827_2 (All); LR P-value: 4.76E-15; mr1827_2 (Jap_All); LR P-value: 8.55E-06; mr1862_2 (All); LR P-value: 3.72E-40; mr1862_2 (Jap_All); LR P-value: 3.56E-09; mr1902_2 (All); LR P-value: 8.63E-15 |
LOC_Os01g56690.1 Alt: A| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 89.451; most accessible tissue: Zhenshan97 flag leaf, score: 97.568 |
| vg0132715485 (J) | chr01 | 32715485 | C | A | 99.90% | 0.00% | C -> A | NA |
LOC_Os01g56690.1 Alt: A| synonymous_variant LOW(snpEff)
The average chromatin accessibility score: 87.755; most accessible tissue: Zhenshan97 flag leaf, score: 96.785 |
| vg0132715492 (J) | chr01 | 32715492 | A | T | 96.60% | 0.00% | A -> T | NA |
LOC_Os01g56690.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 87.654; most accessible tissue: Zhenshan97 flag leaf, score: 96.727 |
| vg0132715707 (J) | chr01 | 32715707 | T | C | 79.60% | 0.00% | T -> C |
Plant_height (All); LR P-value: 5.84E-23;
Plant_height (Ind_All); LR P-value: 2.60E-20; mr1011 (All); LR P-value: 5.46E-08; mr1011 (Ind_All); LR P-value: 2.46E-06; mr1013 (Ind_All); LR P-value: 8.51E-06; mr1014 (Ind_All); LR P-value: 8.55E-07; mr1015 (Ind_All); LR P-value: 1.06E-07; mr1021 (Ind_All); LR P-value: 4.16E-06; mr1031 (All); LR P-value: 5.53E-14; mr1031 (Ind_All); LR P-value: 1.38E-07; mr1032 (Ind_All); LR P-value: 1.08E-06; mr1056 (All); LR P-value: 2.47E-14; mr1056 (Ind_All); LR P-value: 1.19E-07; mr1059 (Ind_All); LR P-value: 9.10E-08; mr1352 (All); LR P-value: 3.13E-09; mr1477 (Ind_All); LR P-value: 8.68E-07; mr1478 (Ind_All); LR P-value: 6.82E-07; mr1675 (Ind_All); LR P-value: 2.24E-09; mr1794 (All); LR P-value: 1.05E-09; mr1950 (Ind_All); LR P-value: 7.37E-07; mr1971 (Ind_All); LR P-value: 6.69E-07; mr1060_2 (All); LR P-value: 1.42E-06; mr1060_2 (Ind_All); LR P-value: 2.83E-10; mr1064_2 (Ind_All); LR P-value: 1.51E-06; mr1156_2 (Ind_All); LR P-value: 7.73E-06; mr1172_2 (All); LR P-value: 3.52E-11; mr1186_2 (All); LR P-value: 5.60E-06; mr1268_2 (All); LR P-value: 2.21E-06; mr1268_2 (Ind_All); LR P-value: 1.96E-08; mr1319_2 (All); LR P-value: 1.92E-11; mr1319_2 (Ind_All); LR P-value: 1.88E-06; mr1327_2 (All); LR P-value: 4.06E-10; mr1327_2 (Ind_All); LR P-value: 5.67E-10; mr1330_2 (All); LR P-value: 4.27E-14; mr1330_2 (Ind_All); LR P-value: 2.65E-07; mr1332_2 (Ind_All); LR P-value: 6.25E-06; mr1338_2 (All); LR P-value: 1.51E-09; mr1346_2 (All); LR P-value: 9.45E-07; mr1352_2 (All); LR P-value: 4.42E-25; mr1352_2 (Ind_All); LR P-value: 2.22E-12; mr1358_2 (Ind_All); LR P-value: 6.75E-06; mr1359_2 (All); LR P-value: 6.18E-06; mr1359_2 (Ind_All); LR P-value: 4.22E-08; mr1378_2 (Ind_All); LR P-value: 2.29E-07; mr1380_2 (Ind_All); LR P-value: 2.77E-06; mr1428_2 (All); LR P-value: 1.24E-08; mr1428_2 (Ind_All); LR P-value: 1.43E-07; mr1439_2 (All); LR P-value: 2.09E-07; mr1454_2 (All); LR P-value: 8.49E-15; mr1454_2 (Ind_All); LR P-value: 4.99E-06; mr1474_2 (Ind_All); LR P-value: 8.21E-06; mr1478_2 (Ind_All); LR P-value: 7.52E-09; mr1579_2 (Ind_All); LR P-value: 3.80E-06; mr1624_2 (Ind_All); LR P-value: 4.63E-07; mr1653_2 (Ind_All); LR P-value: 8.18E-08; mr1830_2 (Ind_All); LR P-value: 3.80E-07; mr1850_2 (All); LR P-value: 3.89E-12; mr1971_2 (Ind_All); LR P-value: 2.13E-07; mr1994_2 (Ind_All); LR P-value: 3.68E-06; mr1996_2 (Ind_All); LR P-value: 1.25E-06 |
LOC_Os01g56690.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 82.430; most accessible tissue: Zhenshan97 flag leaf, score: 93.632 |
| vg0132715982 (J) | chr01 | 32715982 | AT | A | 62.50% | 0.00% | AT -> A | NA |
LOC_Os01g56690.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 72.473; most accessible tissue: Callus, score: 93.175 |
| vg0132716122 (J) | chr01 | 32716122 | C | A | 98.20% | 0.00% | C -> A | NA |
LOC_Os01g56690.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 64.561; most accessible tissue: Zhenshan97 root, score: 89.596 |
| vg0132716343 (J) | chr01 | 32716343 | C | T | 62.20% | 6.37% | C -> T |
mr1090 (Jap_All); LR P-value: 1.31E-06;
mr1097 (All); LR P-value: 2.65E-10; mr1206 (All); LR P-value: 4.31E-07; mr1220 (All); LR P-value: 3.00E-07; mr1229 (All); LR P-value: 1.41E-06; mr1241 (Jap_All); LR P-value: 1.33E-11; mr1248 (All); LR P-value: 8.97E-07; mr1301 (All); LR P-value: 1.73E-18; mr1338 (All); LR P-value: 5.77E-07; mr1425 (All); LR P-value: 4.97E-06; mr1449 (All); LR P-value: 6.30E-15; mr1449 (Jap_All); LR P-value: 1.93E-08; mr1454 (All); LR P-value: 1.18E-11; mr1539 (All); LR P-value: 6.99E-11; mr1540 (All); LR P-value: 1.59E-13; mr1540 (Jap_All); LR P-value: 1.45E-14; mr1642 (All); LR P-value: 4.53E-08; mr1671 (Jap_All); LR P-value: 4.24E-07; mr1699 (All); LR P-value: 4.90E-29; mr1732 (All); LR P-value: 1.55E-15; mr1732 (Jap_All); LR P-value: 2.23E-16; mr1742 (All); LR P-value: 9.42E-07; mr1742 (Jap_All); LR P-value: 2.25E-06; mr1864 (All); LR P-value: 3.36E-11; mr1870 (Jap_All); LR P-value: 5.17E-07; mr1871 (All); LR P-value: 2.16E-13; mr1880 (All); LR P-value: 4.09E-07; mr1993 (All); LR P-value: 1.50E-06; mr1089_2 (Jap_All); LR P-value: 6.08E-10; mr1090_2 (Jap_All); LR P-value: 1.75E-08; mr1092_2 (Jap_All); LR P-value: 8.75E-06; mr1097_2 (All); LR P-value: 8.58E-14; mr1097_2 (Jap_All); LR P-value: 1.20E-07; mr1121_2 (Jap_All); LR P-value: 1.23E-06; mr1206_2 (All); LR P-value: 1.68E-06; mr1211_2 (Jap_All); LR P-value: 4.09E-06; mr1295_2 (All); LR P-value: 5.66E-06; mr1319_2 (Jap_All); LR P-value: 2.18E-06; mr1334_2 (Jap_All); LR P-value: 1.36E-15; mr1363_2 (All); LR P-value: 3.19E-07; mr1471_2 (Jap_All); LR P-value: 7.80E-11; mr1502_2 (All); LR P-value: 7.20E-08; mr1526_2 (Jap_All); LR P-value: 8.76E-09; mr1539_2 (Jap_All); LR P-value: 1.04E-17; mr1540_2 (Jap_All); LR P-value: 8.05E-18; mr1543_2 (All); LR P-value: 5.67E-10; mr1642_2 (All); LR P-value: 4.45E-08; mr1642_2 (Jap_All); LR P-value: 5.68E-09; mr1671_2 (Jap_All); LR P-value: 2.92E-07; mr1679_2 (Jap_All); LR P-value: 5.67E-07; mr1680_2 (All); LR P-value: 1.25E-10; mr1696_2 (All); LR P-value: 7.13E-07; mr1699_2 (All); LR P-value: 2.09E-31; mr1699_2 (Jap_All); LR P-value: 4.70E-17; mr1732_2 (Jap_All); LR P-value: 4.17E-16; mr1742_2 (All); LR P-value: 7.24E-18; mr1742_2 (Jap_All); LR P-value: 4.55E-09; mr1771_2 (Jap_All); LR P-value: 6.89E-10; mr1781_2 (Jap_All); LR P-value: 3.08E-06; mr1784_2 (Jap_All); LR P-value: 2.72E-11; mr1786_2 (All); LR P-value: 5.00E-07; mr1789_2 (Jap_All); LR P-value: 6.13E-11; mr1798_2 (Jap_All); LR P-value: 3.86E-07; mr1817_2 (Jap_All); LR P-value: 2.49E-08; mr1862_2 (Jap_All); LR P-value: 1.42E-09; mr1871_2 (All); LR P-value: 1.73E-21; mr1966_2 (All); LR P-value: 5.41E-07 |
LOC_Os01g56690.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 57.901; most accessible tissue: Zhenshan97 flag leaf, score: 81.008 |
| vg0132716350 (J) | chr01 | 32716350 | TA | T | 74.70% | 0.00% | T -> TA | NA |
The average chromatin accessibility score: 58.870; most accessible tissue: Zhenshan97 flag leaf, score: 82.170
|
| STR0132715251 (J) | chr01 | 32715251 | CATCATC | CATCATT | 84.20% | 0.00% | CATCATC -> CATCATT | NA |
|