23 variations found. Os05g0414300/LOC_Os05g34230 (disease resistance protein RGA3; putative; expressed), ranging from 20,263,660 bp to 20,266,481 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os05g34230 | disease resistance protein RGA3, putative, expressed; RAP ID: Os05g0414300; MSU ID: LOC_Os05g34230 |
The expression data is from the CREP database. And the expression value is log2-transformed. Move the mouse over the cells of the heat map to get detailed tissue information and expression values.
| 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0520263802 (J) | chr05 | 20263802 | G | A | 77.20% | 0.02% | A -> 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 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g34230.1 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_Os05g34240.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g34220.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g34240.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g34240.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 71.181; most accessible tissue: Callus, score: 93.016 |
| vg0520263930 (J) | chr05 | 20263930 | T | C | 77.20% | 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_Os05g34230.1 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_Os05g34240.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g34220.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g34240.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g34240.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 71.475; most accessible tissue: Callus, score: 92.126 |
| vg0520263971 (J) | chr05 | 20263971 | C | G | 77.10% | 0.00% | G -> 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; 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: 3.35E-07; mr1401 (All); LR P-value: 3.27E-15; mr1410 (All); LR P-value: 6.16E-14; mr1422 (All); LR P-value: 2.45E-19; 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: 3.63E-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: 1.59E-23; mr1679 (Jap_All); LR P-value: 1.07E-09; mr1691 (All); LR P-value: 1.92E-09; mr1693 (All); LR P-value: 5.61E-10; mr1699 (Jap_All); LR P-value: 8.76E-19; mr1732 (Jap_All); LR P-value: 5.66E-16; mr1733 (All); LR P-value: 9.39E-35; mr1733 (Jap_All); LR P-value: 5.83E-07; mr1742 (Jap_All); LR P-value: 2.04E-07; mr1845 (All); LR P-value: 2.40E-19; 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: 3.37E-19; mr1539_2 (Jap_All); LR P-value: 1.04E-14; mr1540_2 (All); LR P-value: 6.20E-17; 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: 1.31E-27; mr1679_2 (Jap_All); LR P-value: 1.33E-08; mr1699_2 (Jap_All); LR P-value: 4.98E-19; mr1732_2 (All); LR P-value: 2.21E-16; mr1732_2 (Jap_All); LR P-value: 1.87E-13; mr1733_2 (All); LR P-value: 2.36E-63; mr1733_2 (Jap_All); LR P-value: 1.36E-07; mr1771_2 (All); LR P-value: 1.04E-40; mr1780_2 (Jap_All); LR P-value: 1.71E-06; mr1784_2 (All); LR P-value: 2.79E-43; mr1789_2 (Jap_All); LR P-value: 8.39E-11; mr1790_2 (All); LR P-value: 3.09E-14; 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: 3.98E-16; mr1842_2 (All); LR P-value: 2.54E-16; mr1844_2 (All); LR P-value: 6.11E-11; mr1862_2 (All); LR P-value: 5.26E-39 |
LOC_Os05g34230.1 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_Os05g34240.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g34220.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g34240.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g34240.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 69.813; most accessible tissue: Callus, score: 92.126 |
| vg0520264183 (J) | chr05 | 20264183 | A | T | 77.20% | 0.00% | T -> A |
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_Os05g34230.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g34220.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g34240.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g34220.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g34240.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g34240.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 70.165; most accessible tissue: Callus, score: 92.750 |
| vg0520264655 (J) | chr05 | 20264655 | T | A | 93.40% | 0.00% | T -> A | NA |
LOC_Os05g34230.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 73.073; most accessible tissue: Minghui63 flag leaf, score: 86.315 |
| vg0520264823 (J) | chr05 | 20264823 | G | T | 77.10% | 0.08% | 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; 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: 1.59E-07; mr1410 (All); LR P-value: 3.80E-14; mr1422 (All); LR P-value: 4.56E-19; 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: 1.62E-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: 5.15E-23; mr1679 (Jap_All); LR P-value: 1.07E-09; mr1691 (All); LR P-value: 3.18E-09; mr1693 (All); LR P-value: 7.37E-10; mr1699 (Jap_All); LR P-value: 8.76E-19; mr1732 (Jap_All); LR P-value: 5.66E-16; mr1733 (All); LR P-value: 5.21E-34; mr1733 (Jap_All); LR P-value: 5.83E-07; mr1742 (Jap_All); LR P-value: 2.04E-07; mr1845 (All); LR P-value: 3.39E-19; 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: 8.42E-20; mr1539_2 (Jap_All); LR P-value: 1.04E-14; mr1540_2 (All); LR P-value: 1.28E-17; 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: 4.04E-27; mr1679_2 (Jap_All); LR P-value: 1.33E-08; mr1699_2 (Jap_All); LR P-value: 4.98E-19; mr1732_2 (All); LR P-value: 6.08E-17; mr1732_2 (Jap_All); LR P-value: 1.87E-13; mr1733_2 (All); LR P-value: 1.56E-62; mr1733_2 (Jap_All); LR P-value: 1.36E-07; mr1771_2 (All); LR P-value: 2.67E-41; mr1780_2 (Jap_All); LR P-value: 1.71E-06; mr1784_2 (All); LR P-value: 1.91E-43; mr1789_2 (Jap_All); LR P-value: 8.39E-11; mr1790_2 (All); LR P-value: 4.96E-14; 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: 1.68E-15; mr1842_2 (All); LR P-value: 9.85E-16; mr1844_2 (All); LR P-value: 6.37E-11; mr1862_2 (All); LR P-value: 3.11E-39 |
LOC_Os05g34230.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g34230.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 72.659; most accessible tissue: Zhenshan97 flag leaf, score: 83.366 |
| vg0520264912 (J) | chr05 | 20264912 | 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; 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: 1.00E-07; mr1410 (All); LR P-value: 2.00E-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: 8.14E-08; 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: 1.10E-22; mr1679 (Jap_All); LR P-value: 1.07E-09; mr1691 (All); LR P-value: 5.18E-09; mr1693 (All); LR P-value: 1.06E-09; mr1699 (Jap_All); LR P-value: 8.76E-19; mr1732 (Jap_All); LR P-value: 5.66E-16; mr1733 (All); LR P-value: 2.06E-33; mr1733 (Jap_All); LR P-value: 5.83E-07; mr1742 (Jap_All); LR P-value: 2.04E-07; mr1785 (All); LR P-value: 9.40E-07; mr1845 (All); LR P-value: 1.10E-19; 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; mr1304_2 (All); LR P-value: 4.71E-22; 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: 3.63E-19; mr1539_2 (Jap_All); LR P-value: 1.04E-14; mr1540_2 (All); LR P-value: 3.38E-17; 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: 1.45E-26; mr1679_2 (Jap_All); LR P-value: 1.33E-08; mr1699_2 (Jap_All); LR P-value: 4.98E-19; mr1732_2 (All); LR P-value: 1.90E-16; 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: 1.31E-41; mr1780_2 (Jap_All); LR P-value: 1.71E-06; mr1784_2 (All); LR P-value: 1.16E-43; 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: 6.90E-15; mr1862_2 (All); LR P-value: 1.11E-39 |
LOC_Os05g34230.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 75.850; most accessible tissue: Zhenshan97 flag leaf, score: 88.445 |
| vg0520265229 (J) | chr05 | 20265229 | A | G | 99.90% | 0.00% | A -> G | NA |
LOC_Os05g34230.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os05g34220.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g34240.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g34220.2 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g34240.2 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g34240.3 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 78.019; most accessible tissue: Zhenshan97 flag leaf, score: 91.934 |
| vg0520265441 (J) | chr05 | 20265441 | A | G | 77.20% | 0.00% | G -> A |
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; 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: 3.35E-07; mr1401 (All); LR P-value: 3.27E-15; mr1410 (All); LR P-value: 6.16E-14; mr1422 (All); LR P-value: 2.45E-19; 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: 3.63E-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: 1.59E-23; mr1679 (Jap_All); LR P-value: 1.07E-09; mr1691 (All); LR P-value: 1.92E-09; mr1693 (All); LR P-value: 5.61E-10; mr1699 (Jap_All); LR P-value: 8.76E-19; mr1732 (Jap_All); LR P-value: 5.66E-16; mr1733 (All); LR P-value: 9.39E-35; mr1733 (Jap_All); LR P-value: 5.83E-07; mr1742 (Jap_All); LR P-value: 2.04E-07; mr1845 (All); LR P-value: 2.40E-19; 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: 3.37E-19; mr1539_2 (Jap_All); LR P-value: 1.04E-14; mr1540_2 (All); LR P-value: 6.20E-17; 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: 1.31E-27; mr1679_2 (Jap_All); LR P-value: 1.33E-08; mr1699_2 (Jap_All); LR P-value: 4.98E-19; mr1732_2 (All); LR P-value: 2.21E-16; mr1732_2 (Jap_All); LR P-value: 1.87E-13; mr1733_2 (All); LR P-value: 2.36E-63; mr1733_2 (Jap_All); LR P-value: 1.36E-07; mr1771_2 (All); LR P-value: 1.04E-40; mr1780_2 (Jap_All); LR P-value: 1.71E-06; mr1784_2 (All); LR P-value: 2.79E-43; mr1789_2 (Jap_All); LR P-value: 8.39E-11; mr1790_2 (All); LR P-value: 3.09E-14; 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: 3.98E-16; mr1842_2 (All); LR P-value: 2.54E-16; mr1844_2 (All); LR P-value: 6.11E-11; mr1862_2 (All); LR P-value: 5.26E-39 |
LOC_Os05g34230.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 81.061; most accessible tissue: Minghui63 flag leaf, score: 93.673 |
| vg0520265551 (J) | chr05 | 20265551 | T | C | 94.10% | 0.00% | T -> C | NA |
LOC_Os05g34230.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 83.557; most accessible tissue: Zhenshan97 flag leaf, score: 94.214 |
| vg0520265660 (J) | chr05 | 20265660 | C | T | 77.20% | 0.00% | T -> 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_Os05g34230.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 84.666; most accessible tissue: Minghui63 flag leaf, score: 95.592 |
| vg0520265664 (J) | chr05 | 20265664 | A | G | 77.20% | 0.00% | G -> A |
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_Os05g34230.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 84.784; most accessible tissue: Minghui63 flag leaf, score: 95.545 |
| vg0520265730 (J) | chr05 | 20265730 | C | T | 77.20% | 0.00% | T -> 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; 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: 3.35E-07; mr1401 (All); LR P-value: 3.27E-15; mr1410 (All); LR P-value: 6.16E-14; mr1422 (All); LR P-value: 2.45E-19; 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: 3.63E-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: 1.59E-23; mr1679 (Jap_All); LR P-value: 1.07E-09; mr1691 (All); LR P-value: 1.92E-09; mr1693 (All); LR P-value: 5.61E-10; mr1699 (Jap_All); LR P-value: 8.76E-19; mr1732 (Jap_All); LR P-value: 5.66E-16; mr1733 (All); LR P-value: 9.39E-35; mr1733 (Jap_All); LR P-value: 5.83E-07; mr1742 (Jap_All); LR P-value: 2.04E-07; mr1845 (All); LR P-value: 2.40E-19; 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: 3.37E-19; mr1539_2 (Jap_All); LR P-value: 1.04E-14; mr1540_2 (All); LR P-value: 6.20E-17; 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: 1.31E-27; mr1679_2 (Jap_All); LR P-value: 1.33E-08; mr1699_2 (Jap_All); LR P-value: 4.98E-19; mr1732_2 (All); LR P-value: 2.21E-16; mr1732_2 (Jap_All); LR P-value: 1.87E-13; mr1733_2 (All); LR P-value: 2.36E-63; mr1733_2 (Jap_All); LR P-value: 1.36E-07; mr1771_2 (All); LR P-value: 1.04E-40; mr1780_2 (Jap_All); LR P-value: 1.71E-06; mr1784_2 (All); LR P-value: 2.79E-43; mr1789_2 (Jap_All); LR P-value: 8.39E-11; mr1790_2 (All); LR P-value: 3.09E-14; 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: 3.98E-16; mr1842_2 (All); LR P-value: 2.54E-16; mr1844_2 (All); LR P-value: 6.11E-11; mr1862_2 (All); LR P-value: 5.26E-39 |
LOC_Os05g34230.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 87.981; most accessible tissue: Zhenshan97 flag leaf, score: 96.255 |
| vg0520265747 (J) | chr05 | 20265747 | G | A | 77.20% | 0.04% | A -> 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; 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: 3.35E-07; mr1401 (All); LR P-value: 3.27E-15; mr1410 (All); LR P-value: 6.16E-14; mr1422 (All); LR P-value: 2.45E-19; 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: 3.63E-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: 1.59E-23; mr1679 (Jap_All); LR P-value: 1.07E-09; mr1691 (All); LR P-value: 1.92E-09; mr1693 (All); LR P-value: 5.61E-10; mr1699 (Jap_All); LR P-value: 8.76E-19; mr1732 (Jap_All); LR P-value: 5.66E-16; mr1733 (All); LR P-value: 9.39E-35; mr1733 (Jap_All); LR P-value: 5.83E-07; mr1742 (Jap_All); LR P-value: 2.04E-07; mr1845 (All); LR P-value: 2.40E-19; 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: 3.37E-19; mr1539_2 (Jap_All); LR P-value: 1.04E-14; mr1540_2 (All); LR P-value: 6.20E-17; 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: 1.31E-27; mr1679_2 (Jap_All); LR P-value: 1.33E-08; mr1699_2 (Jap_All); LR P-value: 4.98E-19; mr1732_2 (All); LR P-value: 2.21E-16; mr1732_2 (Jap_All); LR P-value: 1.87E-13; mr1733_2 (All); LR P-value: 2.36E-63; mr1733_2 (Jap_All); LR P-value: 1.36E-07; mr1771_2 (All); LR P-value: 1.04E-40; mr1780_2 (Jap_All); LR P-value: 1.71E-06; mr1784_2 (All); LR P-value: 2.79E-43; mr1789_2 (Jap_All); LR P-value: 8.39E-11; mr1790_2 (All); LR P-value: 3.09E-14; 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: 3.98E-16; mr1842_2 (All); LR P-value: 2.54E-16; mr1844_2 (All); LR P-value: 6.11E-11; mr1862_2 (All); LR P-value: 5.26E-39 |
LOC_Os05g34230.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g34230.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 88.552; most accessible tissue: Zhenshan97 flag leaf, score: 96.488 |
| vg0520265813 (J) | chr05 | 20265813 | G | A | 77.30% | 0.00% | A -> 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_Os05g34230.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 89.667; most accessible tissue: Minghui63 flag leaf, score: 97.049 |
| vg0520265863 (J) | chr05 | 20265863 | C | G | 88.60% | 0.00% | C -> 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_Os05g34230.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 88.082; most accessible tissue: Zhenshan97 flag leaf, score: 97.256 |
| vg0520266085 (J) | chr05 | 20266085 | C | T | 93.40% | 0.00% | C -> T | NA |
LOC_Os05g34230.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 93.091; most accessible tissue: Zhenshan97 flag leaf, score: 98.852 |
| vg0520266191 (J) | chr05 | 20266191 | A | G | 58.90% | 0.00% | G -> A | NA |
LOC_Os05g34230.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 96.625; most accessible tissue: Zhenshan97 flag leaf, score: 99.151 |
| vg0520266236 (J) | chr05 | 20266236 | G | A | 82.60% | 1.44% | G -> A | NA |
LOC_Os05g34230.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g34230.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 97.073; most accessible tissue: Zhenshan97 flag leaf, score: 99.322 |
| vg0520266437 (J) | chr05 | 20266437 | T | C | 88.60% | 0.00% | T -> C |
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_Os05g34230.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g34220.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g34240.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g34220.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g34240.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g34240.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 98.088; most accessible tissue: Zhenshan97 flag leaf, score: 99.484 |
| vg0520266467 (J) | chr05 | 20266467 | T | TCAC | 40.90% | 25.03% | TCAC -> T | NA |
LOC_Os05g34230.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g34220.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g34240.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g34220.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g34240.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g34240.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 97.988; most accessible tissue: Zhenshan97 flag leaf, score: 99.455 |
| vg0520266468 (J) | chr05 | 20266468 | CACA | C | 66.20% | 4.99% | CACA -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g34230.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g34220.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g34240.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g34220.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g34240.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g34240.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 97.987; most accessible tissue: Zhenshan97 flag leaf, score: 99.455 |
| vg0520266471 (J) | chr05 | 20266471 | T | A | 41.80% | 6.83% | A -> T | NA |
LOC_Os05g34230.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g34220.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g34240.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g34220.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g34240.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g34240.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 97.983; most accessible tissue: Zhenshan97 flag leaf, score: 99.453 |