16 variations found. LOC_Os05g34220 (vrga1; putative; expressed), ranging from 20,258,660 bp to 20,262,474 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0520258673 (J) | chr05 | 20258673 | A | G | 58.80% | 0.00% | G -> A | NA |
LOC_Os05g34220.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os05g34220.2 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 98.193; most accessible tissue: Zhenshan97 flag leaf, score: 99.771 |
| vg0520258845 (J) | chr05 | 20258845 | TCGGCGG CGG | TCGG | 74.20% | 0.00% | TCGG -> TCGGCGGCGG ,T | NA |
LOC_Os05g34220.1 Alt: TCGGCGGCGG| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os05g34220.2 Alt: TCGGCGGCGG| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) LOC_Os05g34220.1 Alt: T| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar) LOC_Os05g34220.2 Alt: T| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 95.318; most accessible tissue: Zhenshan97 flag leaf, score: 99.089 |
| vg0520259304 (J) | chr05 | 20259304 | C | A | 77.20% | 0.00% | A -> C |
mr1089 (Jap_All); LR P-value: 6.28E-10;
mr1093 (Jap_All); LR P-value: 2.15E-10; mr1129 (Jap_All); LR P-value: 5.21E-08; mr1217 (All); LR P-value: 5.26E-21; mr1235 (Jap_All); LR P-value: 3.33E-10; mr1251 (Jap_All); LR P-value: 8.34E-10; mr1271 (Jap_All); LR P-value: 1.19E-07; mr1334 (Jap_All); LR P-value: 1.40E-13; mr1364 (All); LR P-value: 2.14E-07; mr1410 (All); LR P-value: 3.25E-14; mr1422 (Jap_All); LR P-value: 1.21E-07; mr1423 (Jap_All); LR P-value: 1.22E-07; mr1435 (Jap_All); LR P-value: 1.48E-10; mr1443 (All); LR P-value: 1.86E-07; mr1539 (Jap_All); LR P-value: 1.88E-10; mr1540 (Jap_All); LR P-value: 3.66E-14; mr1593 (Jap_All); LR P-value: 6.24E-17; mr1629 (Jap_All); LR P-value: 1.38E-06; mr1642 (Jap_All); LR P-value: 8.83E-06; mr1679 (All); LR P-value: 3.42E-23; mr1679 (Jap_All); LR P-value: 1.07E-09; mr1691 (All); LR P-value: 3.15E-09; mr1693 (All); LR P-value: 8.08E-10; mr1699 (Jap_All); LR P-value: 8.76E-19; mr1732 (Jap_All); LR P-value: 5.66E-16; mr1733 (All); LR P-value: 3.77E-34; mr1733 (Jap_All); LR P-value: 5.83E-07; mr1742 (Jap_All); LR P-value: 2.04E-07; mr1845 (All); LR P-value: 7.69E-20; mr1879 (All); LR P-value: 1.08E-11; mr1879 (Jap_All); LR P-value: 7.77E-13; mr1089_2 (Jap_All); LR P-value: 5.97E-11; mr1093_2 (Jap_All); LR P-value: 8.34E-11; mr1235_2 (Jap_All); LR P-value: 4.79E-10; mr1243_2 (Jap_All); LR P-value: 2.61E-06; mr1250_2 (Jap_All); LR P-value: 1.83E-06; mr1251_2 (Jap_All); LR P-value: 2.22E-08; mr1257_2 (Jap_All); LR P-value: 2.88E-07; mr1295_2 (Jap_All); LR P-value: 4.70E-06; mr1334_2 (Jap_All); LR P-value: 7.67E-17; mr1423_2 (Jap_All); LR P-value: 1.07E-07; mr1435_2 (Jap_All); LR P-value: 2.37E-08; mr1471_2 (Jap_All); LR P-value: 3.41E-10; mr1526_2 (Jap_All); LR P-value: 1.06E-07; mr1539_2 (All); LR P-value: 1.42E-18; mr1539_2 (Jap_All); LR P-value: 1.04E-14; mr1540_2 (All); LR P-value: 1.60E-16; mr1540_2 (Jap_All); LR P-value: 4.81E-15; mr1553_2 (Jap_All); LR P-value: 5.53E-06; mr1593_2 (Jap_All); LR P-value: 2.28E-24; mr1599_2 (Jap_All); LR P-value: 4.98E-08; mr1629_2 (Jap_All); LR P-value: 9.26E-07; mr1679_2 (All); LR P-value: 4.77E-27; mr1679_2 (Jap_All); LR P-value: 1.33E-08; mr1699_2 (Jap_All); LR P-value: 4.98E-19; mr1732_2 (Jap_All); LR P-value: 1.87E-13; mr1733_2 (Jap_All); LR P-value: 1.36E-07; mr1771_2 (All); LR P-value: 5.08E-41; mr1780_2 (Jap_All); LR P-value: 1.71E-06; mr1784_2 (All); LR P-value: 1.67E-43; mr1789_2 (All); LR P-value: 1.94E-28; mr1789_2 (Jap_All); LR P-value: 8.39E-11; mr1807_2 (Jap_All); LR P-value: 3.64E-07; mr1817_2 (Jap_All); LR P-value: 1.31E-07; mr1827_2 (All); LR P-value: 1.69E-15; mr1842_2 (All); LR P-value: 5.42E-16; mr1862_2 (All); LR P-value: 1.87E-39 |
LOC_Os05g34220.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os05g34220.2 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 91.878; most accessible tissue: Minghui63 flag leaf, score: 96.221 |
| vg0520259422 (J) | chr05 | 20259422 | A | G | 77.20% | 0.00% | G -> A |
Grain_thickness (All); LR P-value: 1.13E-34;
mr1089 (Jap_All); LR P-value: 3.96E-10; mr1093 (Jap_All); LR P-value: 2.25E-10; mr1129 (Jap_All); LR P-value: 5.16E-08; mr1217 (All); LR P-value: 7.02E-21; mr1235 (Jap_All); LR P-value: 7.96E-11; mr1251 (Jap_All); LR P-value: 7.40E-10; mr1271 (Jap_All); LR P-value: 1.41E-07; mr1401 (All); LR P-value: 1.26E-15; mr1410 (All); LR P-value: 4.40E-14; mr1422 (All); LR P-value: 1.30E-19; mr1422 (Jap_All); LR P-value: 6.06E-08; mr1423 (Jap_All); LR P-value: 4.68E-08; mr1435 (Jap_All); LR P-value: 9.89E-11; mr1443 (All); LR P-value: 4.22E-07; mr1593 (Jap_All); LR P-value: 2.14E-18; mr1599 (Jap_All); LR P-value: 3.20E-07; mr1629 (Jap_All); LR P-value: 2.40E-06; mr1679 (All); LR P-value: 4.43E-23; mr1679 (Jap_All); LR P-value: 2.17E-09; mr1691 (All); LR P-value: 1.73E-09; mr1693 (All); LR P-value: 7.80E-10; mr1699 (Jap_All); LR P-value: 4.35E-17; mr1733 (All); LR P-value: 1.12E-34; mr1742 (Jap_All); LR P-value: 2.12E-06; mr1845 (All); LR P-value: 1.21E-19; mr1879 (Jap_All); LR P-value: 1.33E-12; mr1089_2 (Jap_All); LR P-value: 1.55E-10; mr1093_2 (Jap_All); LR P-value: 2.28E-10; mr1217_2 (All); LR P-value: 1.22E-12; mr1235_2 (Jap_All); LR P-value: 6.47E-10; mr1243_2 (Jap_All); LR P-value: 1.87E-06; mr1257_2 (Jap_All); LR P-value: 7.42E-07; mr1334_2 (Jap_All); LR P-value: 1.10E-15; mr1423_2 (Jap_All); LR P-value: 3.32E-07; mr1539_2 (All); LR P-value: 5.00E-18; mr1593_2 (Jap_All); LR P-value: 4.13E-25; mr1599_2 (Jap_All); LR P-value: 8.81E-08; mr1629_2 (Jap_All); LR P-value: 1.15E-06; mr1679_2 (All); LR P-value: 1.07E-26; mr1679_2 (Jap_All); LR P-value: 5.33E-08; mr1699_2 (Jap_All); LR P-value: 4.15E-17; mr1733_2 (All); LR P-value: 1.47E-62; mr1733_2 (Jap_All); LR P-value: 5.07E-07; mr1771_2 (All); LR P-value: 1.23E-40; mr1780_2 (Jap_All); LR P-value: 1.88E-06; mr1784_2 (All); LR P-value: 8.59E-43; mr1807_2 (Jap_All); LR P-value: 6.64E-07; mr1827_2 (All); LR P-value: 2.24E-15; mr1842_2 (All); LR P-value: 5.19E-16; mr1862_2 (All); LR P-value: 7.63E-39 |
LOC_Os05g34220.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os05g34220.2 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 88.059; most accessible tissue: Zhenshan97 flag leaf, score: 94.419 |
| vg0520259683 (J) | chr05 | 20259683 | T | G | 58.90% | 0.00% | G -> T | NA |
LOC_Os05g34220.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os05g34220.2 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 81.898; most accessible tissue: Zhenshan97 flag leaf, score: 91.470 |
| vg0520259960 (J) | chr05 | 20259960 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os05g34220.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os05g34220.2 Alt: T| synonymous_variant LOW(snpEff) LOC_Os05g34230.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 76.208; most accessible tissue: Zhenshan97 flag leaf, score: 90.298 |
| vg0520260019 (J) | chr05 | 20260019 | C | T | 99.30% | 0.00% | C -> T | NA |
LOC_Os05g34220.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os05g34220.2 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 77.222; most accessible tissue: Zhenshan97 flag leaf, score: 90.004 |
| vg0520260290 (J) | chr05 | 20260290 | A | G | 88.60% | 0.00% | A -> G |
mr1220 (All); LR P-value: 5.52E-07;
mr1248 (All); LR P-value: 5.52E-07; mr1252 (Jap_All); LR P-value: 1.66E-06; mr1271 (All); LR P-value: 8.20E-06; mr1271 (Jap_All); LR P-value: 1.60E-07; mr1301 (All); LR P-value: 2.95E-23; mr1301 (Jap_All); LR P-value: 2.96E-15; mr1338 (All); LR P-value: 1.68E-06; mr1410 (All); LR P-value: 1.36E-13; mr1425 (All); LR P-value: 1.22E-06; mr1449 (All); LR P-value: 1.09E-13; mr1539 (All); LR P-value: 1.39E-09; mr1540 (All); LR P-value: 6.99E-13; mr1540 (Jap_All); LR P-value: 3.58E-15; mr1552 (Jap_All); LR P-value: 6.63E-08; mr1554 (All); LR P-value: 1.15E-08; mr1580 (Jap_All); LR P-value: 1.55E-09; mr1593 (Jap_All); LR P-value: 4.44E-18; mr1642 (All); LR P-value: 8.61E-08; mr1679 (Jap_All); LR P-value: 3.79E-09; mr1699 (All); LR P-value: 2.72E-37; mr1699 (Jap_All); LR P-value: 9.03E-17; mr1732 (All); LR P-value: 5.89E-15; mr1732 (Jap_All); LR P-value: 6.69E-17; mr1742 (All); LR P-value: 8.27E-07; mr1742 (Jap_All); LR P-value: 1.11E-06; mr1871 (All); LR P-value: 1.74E-12; mr1879 (Jap_All); LR P-value: 2.39E-12; mr1916 (Jap_All); LR P-value: 2.34E-07; mr1993 (All); LR P-value: 6.57E-07; mr1993 (Jap_All); LR P-value: 1.32E-07; mr1090_2 (Jap_All); LR P-value: 1.51E-07; mr1097_2 (All); LR P-value: 4.36E-14; mr1097_2 (Jap_All); LR P-value: 1.64E-07; mr1121_2 (Jap_All); LR P-value: 4.35E-07; mr1211_2 (Jap_All); LR P-value: 5.50E-06; mr1250_2 (Jap_All); LR P-value: 2.87E-07; mr1295_2 (All); LR P-value: 1.43E-06; mr1301_2 (All); LR P-value: 2.01E-23; mr1301_2 (Jap_All); LR P-value: 5.60E-16; mr1334_2 (Jap_All); LR P-value: 2.34E-16; mr1363_2 (All); LR P-value: 2.83E-07; mr1410_2 (All); LR P-value: 1.26E-14; mr1502_2 (All); LR P-value: 2.74E-07; mr1526_2 (Jap_All); LR P-value: 2.48E-08; mr1539_2 (Jap_All); LR P-value: 1.19E-15; mr1540_2 (Jap_All); LR P-value: 1.89E-16; mr1543_2 (All); LR P-value: 6.48E-09; mr1574_2 (All); LR P-value: 4.82E-06; mr1593_2 (All); LR P-value: 3.49E-13; mr1593_2 (Jap_All); LR P-value: 1.04E-26; mr1679_2 (Jap_All); LR P-value: 1.12E-07; mr1680_2 (All); LR P-value: 2.18E-10; mr1699_2 (All); LR P-value: 7.39E-38; mr1699_2 (Jap_All); LR P-value: 1.23E-18; mr1732_2 (Jap_All); LR P-value: 1.79E-14; mr1733_2 (Jap_All); LR P-value: 1.93E-07; mr1742_2 (All); LR P-value: 3.12E-15; mr1786_2 (All); LR P-value: 2.20E-07; mr1789_2 (Jap_All); LR P-value: 3.17E-11; mr1807_2 (Jap_All); LR P-value: 4.53E-07; mr1862_2 (Jap_All); LR P-value: 1.14E-08; mr1871_2 (All); LR P-value: 4.19E-21; mr1991_2 (Jap_All); LR P-value: 8.60E-07; mr1993_2 (All); LR P-value: 3.59E-11; mr1993_2 (Jap_All); LR P-value: 6.47E-12 |
LOC_Os05g34220.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os05g34220.2 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 79.744; most accessible tissue: Zhenshan97 young leaf, score: 91.967 |
| vg0520260346 (J) | chr05 | 20260346 | T | G | 77.20% | 0.00% | G -> T |
mr1089 (Jap_All); LR P-value: 6.28E-10;
mr1093 (Jap_All); LR P-value: 2.15E-10; mr1129 (Jap_All); LR P-value: 5.21E-08; mr1217 (All); LR P-value: 5.26E-21; mr1235 (Jap_All); LR P-value: 3.33E-10; mr1251 (Jap_All); LR P-value: 8.34E-10; mr1271 (Jap_All); LR P-value: 1.19E-07; mr1334 (Jap_All); LR P-value: 1.40E-13; mr1364 (All); LR P-value: 2.14E-07; mr1410 (All); LR P-value: 3.25E-14; mr1422 (Jap_All); LR P-value: 1.21E-07; mr1423 (Jap_All); LR P-value: 1.22E-07; mr1435 (Jap_All); LR P-value: 1.48E-10; mr1443 (All); LR P-value: 1.86E-07; mr1539 (Jap_All); LR P-value: 1.88E-10; mr1540 (Jap_All); LR P-value: 3.66E-14; mr1593 (Jap_All); LR P-value: 6.24E-17; mr1629 (Jap_All); LR P-value: 1.38E-06; mr1642 (Jap_All); LR P-value: 8.83E-06; mr1679 (All); LR P-value: 3.42E-23; mr1679 (Jap_All); LR P-value: 1.07E-09; mr1691 (All); LR P-value: 3.15E-09; mr1693 (All); LR P-value: 8.08E-10; mr1699 (Jap_All); LR P-value: 8.76E-19; mr1732 (Jap_All); LR P-value: 5.66E-16; mr1733 (All); LR P-value: 3.77E-34; mr1733 (Jap_All); LR P-value: 5.83E-07; mr1742 (Jap_All); LR P-value: 2.04E-07; mr1845 (All); LR P-value: 7.69E-20; mr1879 (All); LR P-value: 1.08E-11; mr1879 (Jap_All); LR P-value: 7.77E-13; mr1089_2 (Jap_All); LR P-value: 5.97E-11; mr1093_2 (Jap_All); LR P-value: 8.34E-11; mr1235_2 (Jap_All); LR P-value: 4.79E-10; mr1243_2 (Jap_All); LR P-value: 2.61E-06; mr1250_2 (Jap_All); LR P-value: 1.83E-06; mr1251_2 (Jap_All); LR P-value: 2.22E-08; mr1257_2 (Jap_All); LR P-value: 2.88E-07; mr1295_2 (Jap_All); LR P-value: 4.70E-06; mr1334_2 (Jap_All); LR P-value: 7.67E-17; mr1423_2 (Jap_All); LR P-value: 1.07E-07; mr1435_2 (Jap_All); LR P-value: 2.37E-08; mr1471_2 (Jap_All); LR P-value: 3.41E-10; mr1526_2 (Jap_All); LR P-value: 1.06E-07; mr1539_2 (All); LR P-value: 1.42E-18; mr1539_2 (Jap_All); LR P-value: 1.04E-14; mr1540_2 (All); LR P-value: 1.60E-16; mr1540_2 (Jap_All); LR P-value: 4.81E-15; mr1553_2 (Jap_All); LR P-value: 5.53E-06; mr1593_2 (Jap_All); LR P-value: 2.28E-24; mr1599_2 (Jap_All); LR P-value: 4.98E-08; mr1629_2 (Jap_All); LR P-value: 9.26E-07; mr1679_2 (All); LR P-value: 4.77E-27; mr1679_2 (Jap_All); LR P-value: 1.33E-08; mr1699_2 (Jap_All); LR P-value: 4.98E-19; mr1732_2 (Jap_All); LR P-value: 1.87E-13; mr1733_2 (Jap_All); LR P-value: 1.36E-07; mr1771_2 (All); LR P-value: 5.08E-41; mr1780_2 (Jap_All); LR P-value: 1.71E-06; mr1784_2 (All); LR P-value: 1.67E-43; mr1789_2 (All); LR P-value: 1.94E-28; mr1789_2 (Jap_All); LR P-value: 8.39E-11; mr1807_2 (Jap_All); LR P-value: 3.64E-07; mr1817_2 (Jap_All); LR P-value: 1.31E-07; mr1827_2 (All); LR P-value: 1.69E-15; mr1842_2 (All); LR P-value: 5.42E-16; mr1862_2 (All); LR P-value: 1.87E-39 |
LOC_Os05g34220.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os05g34220.2 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 77.828; most accessible tissue: Zhenshan97 young leaf, score: 90.985 |
| vg0520260673 (J) | chr05 | 20260673 | G | C | 77.30% | 0.00% | C -> G |
mr1089 (Jap_All); LR P-value: 6.28E-10;
mr1093 (Jap_All); LR P-value: 2.15E-10; mr1129 (Jap_All); LR P-value: 5.21E-08; mr1217 (All); LR P-value: 5.26E-21; mr1235 (Jap_All); LR P-value: 3.33E-10; mr1251 (Jap_All); LR P-value: 8.34E-10; mr1271 (Jap_All); LR P-value: 1.19E-07; mr1334 (Jap_All); LR P-value: 1.40E-13; mr1364 (All); LR P-value: 2.14E-07; mr1410 (All); LR P-value: 3.25E-14; mr1422 (Jap_All); LR P-value: 1.21E-07; mr1423 (Jap_All); LR P-value: 1.22E-07; mr1435 (Jap_All); LR P-value: 1.48E-10; mr1443 (All); LR P-value: 1.86E-07; mr1539 (Jap_All); LR P-value: 1.88E-10; mr1540 (Jap_All); LR P-value: 3.66E-14; mr1593 (Jap_All); LR P-value: 6.24E-17; mr1629 (Jap_All); LR P-value: 1.38E-06; mr1642 (Jap_All); LR P-value: 8.83E-06; mr1679 (All); LR P-value: 3.42E-23; mr1679 (Jap_All); LR P-value: 1.07E-09; mr1691 (All); LR P-value: 3.15E-09; mr1693 (All); LR P-value: 8.08E-10; mr1699 (Jap_All); LR P-value: 8.76E-19; mr1732 (Jap_All); LR P-value: 5.66E-16; mr1733 (All); LR P-value: 3.77E-34; mr1733 (Jap_All); LR P-value: 5.83E-07; mr1742 (Jap_All); LR P-value: 2.04E-07; mr1845 (All); LR P-value: 7.69E-20; mr1879 (All); LR P-value: 1.08E-11; mr1879 (Jap_All); LR P-value: 7.77E-13; mr1089_2 (Jap_All); LR P-value: 5.97E-11; mr1093_2 (Jap_All); LR P-value: 8.34E-11; mr1235_2 (Jap_All); LR P-value: 4.79E-10; mr1243_2 (Jap_All); LR P-value: 2.61E-06; mr1250_2 (Jap_All); LR P-value: 1.83E-06; mr1251_2 (Jap_All); LR P-value: 2.22E-08; mr1257_2 (Jap_All); LR P-value: 2.88E-07; mr1295_2 (Jap_All); LR P-value: 4.70E-06; mr1334_2 (Jap_All); LR P-value: 7.67E-17; mr1423_2 (Jap_All); LR P-value: 1.07E-07; mr1435_2 (Jap_All); LR P-value: 2.37E-08; mr1471_2 (Jap_All); LR P-value: 3.41E-10; mr1526_2 (Jap_All); LR P-value: 1.06E-07; mr1539_2 (All); LR P-value: 1.42E-18; mr1539_2 (Jap_All); LR P-value: 1.04E-14; mr1540_2 (All); LR P-value: 1.60E-16; mr1540_2 (Jap_All); LR P-value: 4.81E-15; mr1553_2 (Jap_All); LR P-value: 5.53E-06; mr1593_2 (Jap_All); LR P-value: 2.28E-24; mr1599_2 (Jap_All); LR P-value: 4.98E-08; mr1629_2 (Jap_All); LR P-value: 9.26E-07; mr1679_2 (All); LR P-value: 4.77E-27; mr1679_2 (Jap_All); LR P-value: 1.33E-08; mr1699_2 (Jap_All); LR P-value: 4.98E-19; mr1732_2 (Jap_All); LR P-value: 1.87E-13; mr1733_2 (Jap_All); LR P-value: 1.36E-07; mr1771_2 (All); LR P-value: 5.08E-41; mr1780_2 (Jap_All); LR P-value: 1.71E-06; mr1784_2 (All); LR P-value: 1.67E-43; mr1789_2 (All); LR P-value: 1.94E-28; mr1789_2 (Jap_All); LR P-value: 8.39E-11; mr1807_2 (Jap_All); LR P-value: 3.64E-07; mr1817_2 (Jap_All); LR P-value: 1.31E-07; mr1827_2 (All); LR P-value: 1.69E-15; mr1842_2 (All); LR P-value: 5.42E-16; mr1862_2 (All); LR P-value: 1.87E-39 |
LOC_Os05g34220.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os05g34220.2 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 62.824; most accessible tissue: Zhenshan97 flag leaf, score: 80.588 |
| vg0520260896 (J) | chr05 | 20260896 | A | G | 88.60% | 0.00% | A -> G |
mr1220 (All); LR P-value: 5.52E-07;
mr1248 (All); LR P-value: 5.52E-07; mr1252 (Jap_All); LR P-value: 1.66E-06; mr1271 (All); LR P-value: 8.20E-06; mr1271 (Jap_All); LR P-value: 1.60E-07; mr1301 (All); LR P-value: 2.95E-23; mr1301 (Jap_All); LR P-value: 2.96E-15; mr1338 (All); LR P-value: 1.68E-06; mr1410 (All); LR P-value: 1.36E-13; mr1425 (All); LR P-value: 1.22E-06; mr1449 (All); LR P-value: 1.09E-13; mr1539 (All); LR P-value: 1.39E-09; mr1540 (All); LR P-value: 6.99E-13; mr1540 (Jap_All); LR P-value: 3.58E-15; mr1552 (Jap_All); LR P-value: 6.63E-08; mr1554 (All); LR P-value: 1.15E-08; mr1580 (Jap_All); LR P-value: 1.55E-09; mr1593 (Jap_All); LR P-value: 4.44E-18; mr1642 (All); LR P-value: 8.61E-08; mr1679 (Jap_All); LR P-value: 3.79E-09; mr1699 (All); LR P-value: 2.72E-37; mr1699 (Jap_All); LR P-value: 9.03E-17; mr1732 (All); LR P-value: 5.89E-15; mr1732 (Jap_All); LR P-value: 6.69E-17; mr1742 (All); LR P-value: 8.27E-07; mr1742 (Jap_All); LR P-value: 1.11E-06; mr1871 (All); LR P-value: 1.74E-12; mr1879 (Jap_All); LR P-value: 2.39E-12; mr1916 (Jap_All); LR P-value: 2.34E-07; mr1993 (All); LR P-value: 6.57E-07; mr1993 (Jap_All); LR P-value: 1.32E-07; mr1090_2 (Jap_All); LR P-value: 1.51E-07; mr1097_2 (All); LR P-value: 4.36E-14; mr1097_2 (Jap_All); LR P-value: 1.64E-07; mr1121_2 (Jap_All); LR P-value: 4.35E-07; mr1211_2 (Jap_All); LR P-value: 5.50E-06; mr1250_2 (Jap_All); LR P-value: 2.87E-07; mr1295_2 (All); LR P-value: 1.43E-06; mr1301_2 (All); LR P-value: 2.01E-23; mr1301_2 (Jap_All); LR P-value: 5.60E-16; mr1334_2 (Jap_All); LR P-value: 2.34E-16; mr1363_2 (All); LR P-value: 2.83E-07; mr1410_2 (All); LR P-value: 1.26E-14; mr1502_2 (All); LR P-value: 2.74E-07; mr1526_2 (Jap_All); LR P-value: 2.48E-08; mr1539_2 (Jap_All); LR P-value: 1.19E-15; mr1540_2 (Jap_All); LR P-value: 1.89E-16; mr1543_2 (All); LR P-value: 6.48E-09; mr1574_2 (All); LR P-value: 4.82E-06; mr1593_2 (All); LR P-value: 3.49E-13; mr1593_2 (Jap_All); LR P-value: 1.04E-26; mr1679_2 (Jap_All); LR P-value: 1.12E-07; mr1680_2 (All); LR P-value: 2.18E-10; mr1699_2 (All); LR P-value: 7.39E-38; mr1699_2 (Jap_All); LR P-value: 1.23E-18; mr1732_2 (Jap_All); LR P-value: 1.79E-14; mr1733_2 (Jap_All); LR P-value: 1.93E-07; mr1742_2 (All); LR P-value: 3.12E-15; mr1786_2 (All); LR P-value: 2.20E-07; mr1789_2 (Jap_All); LR P-value: 3.17E-11; mr1807_2 (Jap_All); LR P-value: 4.53E-07; mr1862_2 (Jap_All); LR P-value: 1.14E-08; mr1871_2 (All); LR P-value: 4.19E-21; mr1991_2 (Jap_All); LR P-value: 8.60E-07; mr1993_2 (All); LR P-value: 3.59E-11; mr1993_2 (Jap_All); LR P-value: 6.47E-12 |
LOC_Os05g34220.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os05g34220.2 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 58.800; most accessible tissue: Zhenshan97 flag leaf, score: 81.410 |
| vg0520261443 (J) | chr05 | 20261443 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os05g34220.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os05g34220.2 Alt: T| missense_variant MODERATE(snpEff) LOC_Os05g34230.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 74.990; most accessible tissue: Callus, score: 89.526 |
| vg0520262079 (J) | chr05 | 20262079 | T | A | 97.10% | 0.00% | T -> A | NA |
LOC_Os05g34220.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g34220.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g34230.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 77.353; most accessible tissue: Zhenshan97 flag leaf, score: 91.729 |
| vg0520262353 (J) | chr05 | 20262353 | T | C | 77.30% | 0.00% | C -> T |
mr1089 (Jap_All); LR P-value: 6.28E-10;
mr1093 (Jap_All); LR P-value: 2.15E-10; mr1129 (Jap_All); LR P-value: 5.21E-08; mr1217 (All); LR P-value: 5.26E-21; mr1235 (Jap_All); LR P-value: 3.33E-10; mr1251 (Jap_All); LR P-value: 8.34E-10; mr1271 (Jap_All); LR P-value: 1.19E-07; mr1334 (Jap_All); LR P-value: 1.40E-13; mr1364 (All); LR P-value: 2.14E-07; mr1410 (All); LR P-value: 3.25E-14; mr1422 (Jap_All); LR P-value: 1.21E-07; mr1423 (Jap_All); LR P-value: 1.22E-07; mr1435 (Jap_All); LR P-value: 1.48E-10; mr1443 (All); LR P-value: 1.86E-07; mr1539 (Jap_All); LR P-value: 1.88E-10; mr1540 (Jap_All); LR P-value: 3.66E-14; mr1593 (Jap_All); LR P-value: 6.24E-17; mr1629 (Jap_All); LR P-value: 1.38E-06; mr1642 (Jap_All); LR P-value: 8.83E-06; mr1679 (All); LR P-value: 3.42E-23; mr1679 (Jap_All); LR P-value: 1.07E-09; mr1691 (All); LR P-value: 3.15E-09; mr1693 (All); LR P-value: 8.08E-10; mr1699 (Jap_All); LR P-value: 8.76E-19; mr1732 (Jap_All); LR P-value: 5.66E-16; mr1733 (All); LR P-value: 3.77E-34; mr1733 (Jap_All); LR P-value: 5.83E-07; mr1742 (Jap_All); LR P-value: 2.04E-07; mr1845 (All); LR P-value: 7.69E-20; mr1879 (All); LR P-value: 1.08E-11; mr1879 (Jap_All); LR P-value: 7.77E-13; mr1089_2 (Jap_All); LR P-value: 5.97E-11; mr1093_2 (Jap_All); LR P-value: 8.34E-11; mr1235_2 (Jap_All); LR P-value: 4.79E-10; mr1243_2 (Jap_All); LR P-value: 2.61E-06; mr1250_2 (Jap_All); LR P-value: 1.83E-06; mr1251_2 (Jap_All); LR P-value: 2.22E-08; mr1257_2 (Jap_All); LR P-value: 2.88E-07; mr1295_2 (Jap_All); LR P-value: 4.70E-06; mr1334_2 (Jap_All); LR P-value: 7.67E-17; mr1423_2 (Jap_All); LR P-value: 1.07E-07; mr1435_2 (Jap_All); LR P-value: 2.37E-08; mr1471_2 (Jap_All); LR P-value: 3.41E-10; mr1526_2 (Jap_All); LR P-value: 1.06E-07; mr1539_2 (All); LR P-value: 1.42E-18; mr1539_2 (Jap_All); LR P-value: 1.04E-14; mr1540_2 (All); LR P-value: 1.60E-16; mr1540_2 (Jap_All); LR P-value: 4.81E-15; mr1553_2 (Jap_All); LR P-value: 5.53E-06; mr1593_2 (Jap_All); LR P-value: 2.28E-24; mr1599_2 (Jap_All); LR P-value: 4.98E-08; mr1629_2 (Jap_All); LR P-value: 9.26E-07; mr1679_2 (All); LR P-value: 4.77E-27; mr1679_2 (Jap_All); LR P-value: 1.33E-08; mr1699_2 (Jap_All); LR P-value: 4.98E-19; mr1732_2 (Jap_All); LR P-value: 1.87E-13; mr1733_2 (Jap_All); LR P-value: 1.36E-07; mr1771_2 (All); LR P-value: 5.08E-41; mr1780_2 (Jap_All); LR P-value: 1.71E-06; mr1784_2 (All); LR P-value: 1.67E-43; mr1789_2 (All); LR P-value: 1.94E-28; mr1789_2 (Jap_All); LR P-value: 8.39E-11; mr1807_2 (Jap_All); LR P-value: 3.64E-07; mr1817_2 (Jap_All); LR P-value: 1.31E-07; mr1827_2 (All); LR P-value: 1.69E-15; mr1842_2 (All); LR P-value: 5.42E-16; mr1862_2 (All); LR P-value: 1.87E-39 |
LOC_Os05g34220.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g34220.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g34230.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 78.995; most accessible tissue: Zhenshan97 flag leaf, score: 92.013 |
| vg0520262383 (J) | chr05 | 20262383 | G | T | 77.20% | 0.00% | T -> G |
mr1089 (Jap_All); LR P-value: 6.28E-10;
mr1093 (Jap_All); LR P-value: 2.15E-10; mr1129 (Jap_All); LR P-value: 5.21E-08; mr1217 (All); LR P-value: 5.26E-21; mr1235 (Jap_All); LR P-value: 3.33E-10; mr1251 (Jap_All); LR P-value: 8.34E-10; mr1271 (Jap_All); LR P-value: 1.19E-07; mr1334 (Jap_All); LR P-value: 1.40E-13; mr1364 (All); LR P-value: 2.14E-07; mr1410 (All); LR P-value: 3.25E-14; mr1422 (Jap_All); LR P-value: 1.21E-07; mr1423 (Jap_All); LR P-value: 1.22E-07; mr1435 (Jap_All); LR P-value: 1.48E-10; mr1443 (All); LR P-value: 1.86E-07; mr1539 (Jap_All); LR P-value: 1.88E-10; mr1540 (Jap_All); LR P-value: 3.66E-14; mr1593 (Jap_All); LR P-value: 6.24E-17; mr1629 (Jap_All); LR P-value: 1.38E-06; mr1642 (Jap_All); LR P-value: 8.83E-06; mr1679 (All); LR P-value: 3.42E-23; mr1679 (Jap_All); LR P-value: 1.07E-09; mr1691 (All); LR P-value: 3.15E-09; mr1693 (All); LR P-value: 8.08E-10; mr1699 (Jap_All); LR P-value: 8.76E-19; mr1732 (Jap_All); LR P-value: 5.66E-16; mr1733 (All); LR P-value: 3.77E-34; mr1733 (Jap_All); LR P-value: 5.83E-07; mr1742 (Jap_All); LR P-value: 2.04E-07; mr1845 (All); LR P-value: 7.69E-20; mr1879 (All); LR P-value: 1.08E-11; mr1879 (Jap_All); LR P-value: 7.77E-13; mr1089_2 (Jap_All); LR P-value: 5.97E-11; mr1093_2 (Jap_All); LR P-value: 8.34E-11; mr1235_2 (Jap_All); LR P-value: 4.79E-10; mr1243_2 (Jap_All); LR P-value: 2.61E-06; mr1250_2 (Jap_All); LR P-value: 1.83E-06; mr1251_2 (Jap_All); LR P-value: 2.22E-08; mr1257_2 (Jap_All); LR P-value: 2.88E-07; mr1295_2 (Jap_All); LR P-value: 4.70E-06; mr1334_2 (Jap_All); LR P-value: 7.67E-17; mr1423_2 (Jap_All); LR P-value: 1.07E-07; mr1435_2 (Jap_All); LR P-value: 2.37E-08; mr1471_2 (Jap_All); LR P-value: 3.41E-10; mr1526_2 (Jap_All); LR P-value: 1.06E-07; mr1539_2 (All); LR P-value: 1.42E-18; mr1539_2 (Jap_All); LR P-value: 1.04E-14; mr1540_2 (All); LR P-value: 1.60E-16; mr1540_2 (Jap_All); LR P-value: 4.81E-15; mr1553_2 (Jap_All); LR P-value: 5.53E-06; mr1593_2 (Jap_All); LR P-value: 2.28E-24; mr1599_2 (Jap_All); LR P-value: 4.98E-08; mr1629_2 (Jap_All); LR P-value: 9.26E-07; mr1679_2 (All); LR P-value: 4.77E-27; mr1679_2 (Jap_All); LR P-value: 1.33E-08; mr1699_2 (Jap_All); LR P-value: 4.98E-19; mr1732_2 (Jap_All); LR P-value: 1.87E-13; mr1733_2 (Jap_All); LR P-value: 1.36E-07; mr1771_2 (All); LR P-value: 5.08E-41; mr1780_2 (Jap_All); LR P-value: 1.71E-06; mr1784_2 (All); LR P-value: 1.67E-43; mr1789_2 (All); LR P-value: 1.94E-28; mr1789_2 (Jap_All); LR P-value: 8.39E-11; mr1807_2 (Jap_All); LR P-value: 3.64E-07; mr1817_2 (Jap_All); LR P-value: 1.31E-07; mr1827_2 (All); LR P-value: 1.69E-15; mr1842_2 (All); LR P-value: 5.42E-16; mr1862_2 (All); LR P-value: 1.87E-39 |
LOC_Os05g34220.2 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g34220.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g34230.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 79.698; most accessible tissue: Zhenshan97 flag leaf, score: 91.854 |
| vg0520262388 (J) | chr05 | 20262388 | T | C | 93.40% | 0.00% | T -> C | NA |
LOC_Os05g34220.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g34220.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g34230.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 79.141; most accessible tissue: Zhenshan97 flag leaf, score: 91.557 |