20 variations found. LOC_Os02g58550 (chloroplast channel forming outer membrane protein; putative; expressed), ranging from 35,784,841 bp to 35,787,820 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 |
|---|---|---|---|---|---|---|---|---|---|
| STR0235787007 (J) | chr02 | 35787007 | ATATATA TATA | ATATATA TATA | 99.00% | 0.00% | ATATATATAT A -> ATATATATAT ATA | NA |
|
| vg0235785144 (J) | chr02 | 35785144 | G | A | 68.90% | 0.00% | G -> A |
Heading_date (Ind_All); LR P-value: 9.52E-10;
mr1125_2 (Ind_All); LR P-value: 1.86E-08; mr1498_2 (All); LR P-value: 3.54E-07; mr1924_2 (Ind_All); LR P-value: 1.66E-06 |
LOC_Os02g58540.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g58554.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58530.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58550.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58550.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.926; most accessible tissue: Minghui63 root, score: 90.280 |
| vg0235785343 (J) | chr02 | 35785343 | T | C | 59.40% | 0.00% | C -> T |
mr1021 (All); LR P-value: 1.01E-19;
mr1029 (All); LR P-value: 4.89E-06; mr1047 (All); LR P-value: 4.82E-10; mr1189 (All); LR P-value: 3.32E-06; mr1325 (All); LR P-value: 3.90E-11; mr1326 (All); LR P-value: 3.08E-13; mr1580 (All); LR P-value: 1.58E-20; mr1625 (All); LR P-value: 9.45E-06; mr1657 (All); LR P-value: 3.05E-11; mr1744 (All); LR P-value: 1.31E-12; mr1796 (All); LR P-value: 1.53E-07; mr1064_2 (All); LR P-value: 4.60E-59; mr1208_2 (All); LR P-value: 8.37E-37; mr1270_2 (All); LR P-value: 4.57E-28; mr1316_2 (All); LR P-value: 1.30E-22; mr1323_2 (All); LR P-value: 5.20E-28; mr1325_2 (All); LR P-value: 1.73E-12; mr1326_2 (All); LR P-value: 6.74E-14; mr1744_2 (All); LR P-value: 2.27E-17; mr1745_2 (All); LR P-value: 6.72E-40; mr1782_2 (All); LR P-value: 1.16E-10; mr1932_2 (All); LR P-value: 1.90E-30; mr1970_2 (All); LR P-value: 2.24E-65; mr1973_2 (All); LR P-value: 4.24E-104 |
LOC_Os02g58540.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g58554.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58530.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58550.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58550.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.475; most accessible tissue: Minghui63 panicle, score: 89.175 |
| vg0235785444 (J) | chr02 | 35785444 | C | T | 59.50% | 0.00% | T -> C |
mr1021 (All); LR P-value: 1.01E-19;
mr1029 (All); LR P-value: 4.89E-06; mr1047 (All); LR P-value: 4.82E-10; mr1189 (All); LR P-value: 3.32E-06; mr1325 (All); LR P-value: 3.90E-11; mr1326 (All); LR P-value: 3.08E-13; mr1580 (All); LR P-value: 1.58E-20; mr1625 (All); LR P-value: 9.45E-06; mr1657 (All); LR P-value: 3.05E-11; mr1744 (All); LR P-value: 1.31E-12; mr1796 (All); LR P-value: 1.53E-07; mr1064_2 (All); LR P-value: 4.60E-59; mr1208_2 (All); LR P-value: 8.37E-37; mr1270_2 (All); LR P-value: 4.57E-28; mr1316_2 (All); LR P-value: 1.30E-22; mr1323_2 (All); LR P-value: 5.20E-28; mr1325_2 (All); LR P-value: 1.73E-12; mr1326_2 (All); LR P-value: 6.74E-14; mr1744_2 (All); LR P-value: 2.27E-17; mr1745_2 (All); LR P-value: 6.72E-40; mr1782_2 (All); LR P-value: 1.16E-10; mr1932_2 (All); LR P-value: 1.90E-30; mr1970_2 (All); LR P-value: 2.24E-65; mr1973_2 (All); LR P-value: 4.24E-104 |
LOC_Os02g58540.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g58554.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58530.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58550.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58550.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 82.718; most accessible tissue: Callus, score: 93.800 |
| vg0235785700 (J) | chr02 | 35785700 | G | T | 59.50% | 0.00% | T -> G |
mr1021 (All); LR P-value: 1.01E-19;
mr1029 (All); LR P-value: 4.89E-06; mr1047 (All); LR P-value: 4.82E-10; mr1189 (All); LR P-value: 3.32E-06; mr1325 (All); LR P-value: 3.90E-11; mr1326 (All); LR P-value: 3.08E-13; mr1580 (All); LR P-value: 1.58E-20; mr1625 (All); LR P-value: 9.45E-06; mr1657 (All); LR P-value: 3.05E-11; mr1744 (All); LR P-value: 1.31E-12; mr1796 (All); LR P-value: 1.53E-07; mr1064_2 (All); LR P-value: 4.60E-59; mr1208_2 (All); LR P-value: 8.37E-37; mr1270_2 (All); LR P-value: 4.57E-28; mr1316_2 (All); LR P-value: 1.30E-22; mr1323_2 (All); LR P-value: 5.20E-28; mr1325_2 (All); LR P-value: 1.73E-12; mr1326_2 (All); LR P-value: 6.74E-14; mr1744_2 (All); LR P-value: 2.27E-17; mr1745_2 (All); LR P-value: 6.72E-40; mr1782_2 (All); LR P-value: 1.16E-10; mr1932_2 (All); LR P-value: 1.90E-30; mr1970_2 (All); LR P-value: 2.24E-65; mr1973_2 (All); LR P-value: 4.24E-104 |
LOC_Os02g58540.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g58554.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58530.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58550.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58550.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 88.956; most accessible tissue: Callus, score: 95.779 |
| vg0235785718 (J) | chr02 | 35785718 | G | A | 59.40% | 0.00% | A -> G |
mr1021 (All); LR P-value: 1.84E-19;
mr1047 (All); LR P-value: 7.66E-10; mr1189 (All); LR P-value: 9.38E-06; mr1325 (All); LR P-value: 2.74E-11; mr1326 (All); LR P-value: 7.89E-13; mr1580 (All); LR P-value: 1.31E-20; mr1734 (All); LR P-value: 8.19E-06; mr1744 (All); LR P-value: 2.02E-12; mr1796 (All); LR P-value: 5.43E-07; mr1064_2 (All); LR P-value: 9.64E-59; mr1270_2 (All); LR P-value: 5.96E-27; mr1323_2 (All); LR P-value: 3.39E-28; mr1325_2 (All); LR P-value: 1.18E-12; mr1326_2 (All); LR P-value: 5.17E-14; mr1526_2 (All); LR P-value: 6.54E-57; mr1744_2 (All); LR P-value: 2.19E-17; mr1782_2 (All); LR P-value: 1.78E-10; mr1932_2 (All); LR P-value: 1.73E-29; mr1970_2 (All); LR P-value: 3.52E-62; mr1973_2 (All); LR P-value: 4.99E-99 |
LOC_Os02g58540.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g58554.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58530.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58550.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58550.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 88.788; most accessible tissue: Callus, score: 95.779 |
| vg0235785952 (J) | chr02 | 35785952 | T | A | 99.60% | 0.00% | T -> A | NA |
LOC_Os02g58550.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os02g58540.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g58554.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g58530.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g58550.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 80.830; most accessible tissue: Zhenshan97 flower, score: 92.192 |
| vg0235786095 (J) | chr02 | 35786095 | G | T | 59.50% | 0.00% | T -> G |
mr1029 (All); LR P-value: 5.43E-06;
mr1047 (All); LR P-value: 6.82E-10; mr1189 (All); LR P-value: 4.89E-06; mr1325 (All); LR P-value: 7.07E-11; mr1580 (All); LR P-value: 6.54E-20; mr1625 (All); LR P-value: 8.35E-06; mr1657 (All); LR P-value: 2.22E-11; mr1744 (All); LR P-value: 2.58E-12; mr1796 (All); LR P-value: 2.88E-07; mr1064_2 (All); LR P-value: 5.07E-58; mr1323_2 (All); LR P-value: 8.23E-28; mr1744_2 (All); LR P-value: 5.99E-17; mr1745_2 (All); LR P-value: 2.08E-38; mr1782_2 (All); LR P-value: 3.51E-10; mr1932_2 (All); LR P-value: 2.87E-29; mr1970_2 (All); LR P-value: 2.74E-62; mr1973_2 (All); LR P-value: 2.29E-98 |
LOC_Os02g58550.2 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g58540.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58554.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58530.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58550.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 61.234; most accessible tissue: Zhenshan97 flower, score: 81.047 |
| vg0235786238 (J) | chr02 | 35786238 | A | T | 59.50% | 0.00% | T -> A |
mr1021 (All); LR P-value: 1.25E-19;
mr1029 (All); LR P-value: 3.27E-06; mr1047 (All); LR P-value: 2.74E-10; mr1189 (All); LR P-value: 2.23E-06; mr1325 (All); LR P-value: 4.49E-11; mr1326 (All); LR P-value: 1.82E-13; mr1580 (All); LR P-value: 1.04E-19; mr1625 (All); LR P-value: 5.70E-06; mr1657 (All); LR P-value: 7.81E-12; mr1744 (All); LR P-value: 1.36E-12; mr1782 (All); LR P-value: 8.58E-06; mr1796 (All); LR P-value: 8.96E-08; mr1990 (All); LR P-value: 1.75E-06; mr1064_2 (All); LR P-value: 5.89E-59; mr1270_2 (All); LR P-value: 8.48E-28; mr1316_2 (All); LR P-value: 1.18E-22; mr1323_2 (All); LR P-value: 1.70E-28; mr1325_2 (All); LR P-value: 1.51E-12; mr1326_2 (All); LR P-value: 5.17E-14; mr1744_2 (All); LR P-value: 3.45E-17; mr1745_2 (All); LR P-value: 2.15E-38; mr1782_2 (All); LR P-value: 1.21E-10; mr1932_2 (All); LR P-value: 3.62E-30; mr1970_2 (All); LR P-value: 2.56E-63; mr1973_2 (All); LR P-value: 1.47E-100 |
LOC_Os02g58540.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g58554.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58530.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58550.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58550.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 59.176; most accessible tissue: Callus, score: 79.979 |
| vg0235786272 (J) | chr02 | 35786272 | T | C | 59.60% | 0.00% | C -> T |
mr1021 (All); LR P-value: 5.39E-20;
mr1029 (All); LR P-value: 6.31E-06; mr1047 (All); LR P-value: 3.59E-10; mr1189 (All); LR P-value: 3.34E-06; mr1325 (All); LR P-value: 3.25E-11; mr1326 (All); LR P-value: 1.36E-13; mr1580 (All); LR P-value: 8.83E-20; mr1657 (All); LR P-value: 1.35E-11; mr1744 (All); LR P-value: 1.80E-12; mr1796 (All); LR P-value: 1.28E-07; mr1990 (All); LR P-value: 2.67E-06; mr1064_2 (All); LR P-value: 3.18E-59; mr1270_2 (All); LR P-value: 6.42E-28; mr1316_2 (All); LR P-value: 2.42E-22; mr1323_2 (All); LR P-value: 7.96E-29; mr1325_2 (All); LR P-value: 1.23E-12; mr1326_2 (All); LR P-value: 4.98E-14; mr1744_2 (All); LR P-value: 1.29E-17; mr1781_2 (All); LR P-value: 6.28E-11; mr1782_2 (All); LR P-value: 1.22E-10; mr1932_2 (All); LR P-value: 2.24E-30; mr1970_2 (All); LR P-value: 1.00E-63; mr1973_2 (All); LR P-value: 1.87E-101 |
LOC_Os02g58540.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g58554.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58530.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58550.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58550.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 60.113; most accessible tissue: Callus, score: 79.979 |
| vg0235786773 (J) | chr02 | 35786773 | C | A | 89.20% | 0.00% | A -> C |
Heading_date (All); LR P-value: 2.92E-11;
Heading_date (Jap_All); LR P-value: 3.70E-11; Plant_height (Jap_All); LR P-value: 1.65E-12; Spikelet_length (Jap_All); LR P-value: 4.24E-11; mr1002 (All); LR P-value: 6.71E-09; mr1002 (Jap_All); LR P-value: 1.38E-07; mr1182 (Jap_All); LR P-value: 7.40E-06; mr1002_2 (All); LR P-value: 4.08E-12; mr1002_2 (Jap_All); LR P-value: 1.21E-09; mr1010_2 (All); LR P-value: 2.73E-22; mr1010_2 (Jap_All); LR P-value: 2.69E-10; mr1077_2 (Jap_All); LR P-value: 3.16E-06; mr1164_2 (Jap_All); LR P-value: 4.48E-06; mr1229_2 (All); LR P-value: 6.81E-07; mr1263_2 (All); LR P-value: 6.46E-06; mr1263_2 (Jap_All); LR P-value: 5.10E-06; mr1338_2 (Jap_All); LR P-value: 2.37E-07; mr1354_2 (Jap_All); LR P-value: 2.43E-06; mr1359_2 (Jap_All); LR P-value: 4.93E-08; mr1380_2 (Jap_All); LR P-value: 6.43E-06; mr1627_2 (Jap_All); LR P-value: 1.90E-06; mr1709_2 (Jap_All); LR P-value: 2.23E-09; mr1763_2 (All); LR P-value: 8.03E-06; mr1829_2 (All); LR P-value: 1.62E-08; mr1880_2 (All); LR P-value: 2.99E-08; mr1902_2 (All); LR P-value: 1.55E-15; mr1902_2 (Jap_All); LR P-value: 1.40E-06; mr1952_2 (All); LR P-value: 2.70E-07; mr1977_2 (All); LR P-value: 7.82E-07; mr1977_2 (Jap_All); LR P-value: 9.73E-06 |
LOC_Os02g58540.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g58554.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58550.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58550.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 85.367; most accessible tissue: Minghui63 flower, score: 91.834 |
| vg0235786857 (J) | chr02 | 35786857 | G | A | 59.50% | 0.00% | A -> G |
mr1021 (All); LR P-value: 1.28E-19;
mr1047 (All); LR P-value: 1.45E-09; mr1189 (All); LR P-value: 6.52E-06; mr1325 (All); LR P-value: 4.57E-11; mr1326 (All); LR P-value: 3.81E-13; mr1580 (All); LR P-value: 3.87E-20; mr1744 (All); LR P-value: 4.99E-13; mr1796 (All); LR P-value: 2.72E-07; mr1841 (All); LR P-value: 4.28E-23; mr1064_2 (All); LR P-value: 1.88E-59; mr1208_2 (All); LR P-value: 9.48E-38; mr1270_2 (All); LR P-value: 1.78E-28; mr1316_2 (All); LR P-value: 7.59E-24; mr1323_2 (All); LR P-value: 5.57E-27; mr1325_2 (All); LR P-value: 3.17E-12; mr1326_2 (All); LR P-value: 5.66E-14; mr1526_2 (All); LR P-value: 4.58E-57; mr1744_2 (All); LR P-value: 6.77E-17; mr1745_2 (All); LR P-value: 5.22E-40; mr1782_2 (All); LR P-value: 2.98E-10; mr1925_2 (All); LR P-value: 2.37E-06; mr1932_2 (All); LR P-value: 8.35E-31; mr1970_2 (All); LR P-value: 1.64E-64; mr1973_2 (All); LR P-value: 6.40E-104 |
LOC_Os02g58540.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g58554.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58550.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58550.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 84.640; most accessible tissue: Minghui63 flower, score: 92.842 |
| vg0235787006 (J) | chr02 | 35787006 | C | CAT | 98.60% | 0.00% | C -> CAT | NA |
LOC_Os02g58540.1 Alt: CAT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g58554.1 Alt: CAT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58550.1 Alt: CAT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58550.2 Alt: CAT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 91.037; most accessible tissue: Minghui63 flower, score: 94.846 |
| vg0235787142 (J) | chr02 | 35787142 | G | A | 98.40% | 0.00% | G -> A |
LOC_Os02g58550.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g58550.2 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 93.341; most accessible tissue: Minghui63 flower, score: 96.493 |
|
| vg0235787144 (J) | chr02 | 35787144 | T | C | 59.50% | 0.00% | C -> T |
mr1021 (All); LR P-value: 1.51E-19;
mr1029 (All); LR P-value: 3.87E-06; mr1047 (All); LR P-value: 4.61E-10; mr1189 (All); LR P-value: 3.15E-06; mr1325 (All); LR P-value: 5.30E-11; mr1326 (All); LR P-value: 4.55E-13; mr1580 (All); LR P-value: 1.49E-20; mr1625 (All); LR P-value: 7.87E-06; mr1657 (All); LR P-value: 4.66E-11; mr1744 (All); LR P-value: 1.24E-12; mr1796 (All); LR P-value: 1.49E-07; mr1990 (All); LR P-value: 3.58E-06; mr1064_2 (All); LR P-value: 1.06E-58; mr1208_2 (All); LR P-value: 1.05E-36; mr1270_2 (All); LR P-value: 5.47E-28; mr1316_2 (All); LR P-value: 7.11E-23; mr1323_2 (All); LR P-value: 1.80E-27; mr1325_2 (All); LR P-value: 1.67E-12; mr1326_2 (All); LR P-value: 6.11E-14; mr1744_2 (All); LR P-value: 4.78E-17; mr1745_2 (All); LR P-value: 4.02E-40; mr1782_2 (All); LR P-value: 1.29E-10; mr1932_2 (All); LR P-value: 3.40E-30; mr1970_2 (All); LR P-value: 4.04E-65; mr1973_2 (All); LR P-value: 1.26E-103 |
LOC_Os02g58550.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g58550.2 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 93.198; most accessible tissue: Minghui63 flower, score: 96.397 |
| vg0235787188 (J) | chr02 | 35787188 | T | C | 98.60% | 0.00% | T -> C | NA |
LOC_Os02g58540.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g58554.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58550.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58550.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 94.352; most accessible tissue: Minghui63 flower, score: 96.735 |
| vg0235787325 (J) | chr02 | 35787325 | G | A | 59.50% | 0.00% | A -> G |
mr1021 (All); LR P-value: 1.69E-19;
mr1029 (All); LR P-value: 3.86E-06; mr1047 (All); LR P-value: 5.14E-10; mr1189 (All); LR P-value: 2.68E-06; mr1325 (All); LR P-value: 1.48E-11; mr1326 (All); LR P-value: 1.11E-13; mr1580 (All); LR P-value: 2.94E-20; mr1625 (All); LR P-value: 7.06E-06; mr1657 (All); LR P-value: 1.26E-11; mr1744 (All); LR P-value: 1.23E-12; mr1796 (All); LR P-value: 1.19E-07; mr1990 (All); LR P-value: 3.67E-06; mr1064_2 (All); LR P-value: 2.86E-58; mr1270_2 (All); LR P-value: 2.32E-27; mr1316_2 (All); LR P-value: 2.32E-22; mr1323_2 (All); LR P-value: 3.05E-28; mr1325_2 (All); LR P-value: 1.41E-12; mr1326_2 (All); LR P-value: 5.78E-14; mr1744_2 (All); LR P-value: 2.44E-17; mr1745_2 (All); LR P-value: 3.31E-39; mr1782_2 (All); LR P-value: 1.71E-10; mr1932_2 (All); LR P-value: 8.35E-30; mr1970_2 (All); LR P-value: 1.80E-63; mr1973_2 (All); LR P-value: 1.41E-100 |
LOC_Os02g58550.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g58550.2 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 95.557; most accessible tissue: Zhenshan97 flower, score: 97.794 |
| vg0235787722 (J) | chr02 | 35787722 | AGGGTTT GGGTTT | A | 57.30% | 0.00% | A -> AGGGTTTGGG TTT | NA |
LOC_Os02g58550.1 Alt: AGGGTTTGGGTTT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g58550.2 Alt: AGGGTTTGGGTTT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58540.1 Alt: AGGGTTTGGGTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58554.1 Alt: AGGGTTTGGGTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 98.737; most accessible tissue: Callus, score: 99.838 |
| vg0235787729 (J) | chr02 | 35787729 | A | G | 99.80% | 0.00% | A -> G | NA |
LOC_Os02g58550.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os02g58550.2 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os02g58540.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g58554.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 98.735; most accessible tissue: Callus, score: 99.838 |
| vg0235787732 (J) | chr02 | 35787732 | A | T | 99.80% | 0.00% | A -> T | NA |
LOC_Os02g58550.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os02g58550.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os02g58540.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g58554.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 98.743; most accessible tissue: Callus, score: 99.838 |
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