13 variations found. Os05g0548700/LOC_Os05g47520 (expressed protein), ranging from 27,222,700 bp to 27,223,643 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os05g47520 | hypothetical protein; RAP ID: Os05g0548700; MSU ID: LOC_Os05g47520 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0527222754 (J) | chr05 | 27222754 | C | T | 53.00% | 0.02% | C -> T | NA |
LOC_Os05g47520.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os05g47520.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 86.702; most accessible tissue: Zhenshan97 flower, score: 91.514 |
| vg0527222863 (J) | chr05 | 27222863 | C | CAT | 89.10% | 0.08% | C -> CAT | NA |
LOC_Os05g47520.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g47520.1 Alt: CAT| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 87.380; most accessible tissue: Minghui63 flag leaf, score: 93.138 |
| vg0527223175 (J) | chr05 | 27223175 | GTC | G | 99.70% | 0.00% | GTC -> G | NA |
LOC_Os05g47520.1 Alt: G| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 91.820; most accessible tissue: Zhenshan97 flower, score: 95.508 |
| vg0527223176 (J) | chr05 | 27223176 | G | T | 79.50% | 0.00% | T -> G |
mr1115 (Jap_All); LR P-value: 4.77E-16;
mr1241 (Jap_All); LR P-value: 1.42E-11; mr1448 (Jap_All); LR P-value: 4.66E-06; mr1611 (All); LR P-value: 1.44E-22; mr1611 (Jap_All); LR P-value: 3.00E-13; mr1629 (Jap_All); LR P-value: 1.23E-07; mr1858 (Jap_All); LR P-value: 8.82E-06; mr1859 (Jap_All); LR P-value: 8.85E-06; mr1920 (All); LR P-value: 6.29E-23; mr1920 (Jap_All); LR P-value: 8.80E-12; mr1156_2 (Jap_All); LR P-value: 5.07E-08; mr1189_2 (Jap_All); LR P-value: 8.63E-09; mr1228_2 (All); LR P-value: 5.68E-10; mr1241_2 (All); LR P-value: 4.99E-58; mr1241_2 (Jap_All); LR P-value: 6.81E-13; mr1246_2 (Jap_All); LR P-value: 6.81E-06; mr1308_2 (All); LR P-value: 1.76E-20; mr1361_2 (All); LR P-value: 5.03E-22; mr1364_2 (All); LR P-value: 2.43E-09; mr1364_2 (Jap_All); LR P-value: 1.78E-10; mr1383_2 (Jap_All); LR P-value: 8.73E-07; mr1454_2 (Jap_All); LR P-value: 4.43E-09; mr1471_2 (Jap_All); LR P-value: 2.63E-11; mr1543_2 (Jap_All); LR P-value: 5.33E-09; mr1642_2 (Jap_All); LR P-value: 1.36E-09; mr1793_2 (Jap_All); LR P-value: 9.06E-06; mr1825_2 (Jap_All); LR P-value: 1.60E-09; mr1980_2 (All); LR P-value: 1.69E-18; mr1993_2 (All); LR P-value: 4.84E-10 |
LOC_Os05g47520.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 91.820; most accessible tissue: Zhenshan97 flower, score: 95.508 |
| vg0527223177 (J) | chr05 | 27223177 | A | C | 79.50% | 0.00% | C -> A,CGAGGA |
mr1115 (Jap_All); LR P-value: 4.77E-16;
mr1241 (Jap_All); LR P-value: 1.42E-11; mr1448 (Jap_All); LR P-value: 4.66E-06; mr1611 (All); LR P-value: 1.44E-22; mr1611 (Jap_All); LR P-value: 3.00E-13; mr1629 (Jap_All); LR P-value: 1.23E-07; mr1858 (Jap_All); LR P-value: 8.82E-06; mr1859 (Jap_All); LR P-value: 8.85E-06; mr1920 (All); LR P-value: 6.29E-23; mr1920 (Jap_All); LR P-value: 8.80E-12; mr1156_2 (Jap_All); LR P-value: 5.07E-08; mr1189_2 (Jap_All); LR P-value: 8.63E-09; mr1228_2 (All); LR P-value: 5.68E-10; mr1241_2 (All); LR P-value: 4.99E-58; mr1241_2 (Jap_All); LR P-value: 6.81E-13; mr1246_2 (Jap_All); LR P-value: 6.81E-06; mr1308_2 (All); LR P-value: 1.76E-20; mr1361_2 (All); LR P-value: 5.03E-22; mr1364_2 (All); LR P-value: 2.43E-09; mr1364_2 (Jap_All); LR P-value: 1.78E-10; mr1383_2 (Jap_All); LR P-value: 8.73E-07; mr1454_2 (Jap_All); LR P-value: 4.43E-09; mr1471_2 (Jap_All); LR P-value: 2.63E-11; mr1543_2 (Jap_All); LR P-value: 5.33E-09; mr1642_2 (Jap_All); LR P-value: 1.36E-09; mr1793_2 (Jap_All); LR P-value: 9.06E-06; mr1825_2 (Jap_All); LR P-value: 1.60E-09; mr1980_2 (All); LR P-value: 1.69E-18; mr1993_2 (All); LR P-value: 4.84E-10 |
LOC_Os05g47520.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os05g47520.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os05g47520.1 Alt: CGAGGA| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 91.952; most accessible tissue: Zhenshan97 flower, score: 95.612 |
| vg0527223220 (J) | chr05 | 27223220 | G | C | 95.10% | 0.00% | G -> C |
mr1101 (All); LR P-value: 7.10E-26;
mr1166 (All); LR P-value: 3.17E-14; mr1168 (All); LR P-value: 1.29E-21; mr1210 (All); LR P-value: 1.06E-22; mr1231 (All); LR P-value: 6.42E-13; mr1305 (All); LR P-value: 6.33E-26; mr1465 (All); LR P-value: 1.18E-08; mr1515 (All); LR P-value: 2.09E-22; mr1549 (All); LR P-value: 1.52E-37; mr1550 (All); LR P-value: 4.79E-43; mr1556 (All); LR P-value: 1.59E-06; mr1586 (All); LR P-value: 5.78E-28; mr1633 (All); LR P-value: 3.40E-06; mr1649 (All); LR P-value: 2.14E-11; mr1706 (All); LR P-value: 1.37E-07; mr1764 (All); LR P-value: 4.06E-07; mr1774 (All); LR P-value: 6.81E-06; mr1817 (All); LR P-value: 2.17E-20; mr1858 (All); LR P-value: 5.88E-27; mr1859 (All); LR P-value: 5.47E-27; mr1897 (All); LR P-value: 4.29E-13; mr1927 (All); LR P-value: 3.49E-10; mr1939 (All); LR P-value: 1.15E-08; mr1047_2 (All); LR P-value: 6.69E-10; mr1193_2 (All); LR P-value: 2.33E-10; mr1305_2 (All); LR P-value: 1.31E-20; mr1344_2 (All); LR P-value: 3.39E-07; mr1409_2 (All); LR P-value: 1.29E-11; mr1510_2 (All); LR P-value: 1.49E-08; mr1530_2 (All); LR P-value: 1.00E-15; mr1549_2 (All); LR P-value: 4.16E-34; mr1550_2 (All); LR P-value: 5.86E-47; mr1587_2 (All); LR P-value: 2.38E-16; mr1757_2 (All); LR P-value: 6.10E-27; mr1803_2 (All); LR P-value: 2.85E-13; mr1808_2 (All); LR P-value: 3.50E-08; mr1815_2 (All); LR P-value: 2.03E-06 |
LOC_Os05g47520.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 92.414; most accessible tissue: Zhenshan97 flower, score: 96.532 |
| vg0527223361 (J) | chr05 | 27223361 | G | C | 98.60% | 0.00% | G -> C | NA |
LOC_Os05g47510.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g47530.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g47520.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 91.027; most accessible tissue: Zhenshan97 flower, score: 97.125 |
| vg0527223421 (J) | chr05 | 27223421 | C | G | 53.00% | 0.11% | C -> G | NA |
LOC_Os05g47520.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g47520.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 91.192; most accessible tissue: Zhenshan97 flower, score: 96.899 |
| vg0527223439 (J) | chr05 | 27223439 | A | C | 89.30% | 0.00% | A -> C |
mr1016 (Ind_All); LR P-value: 2.44E-13;
mr1022 (Ind_All); LR P-value: 2.69E-15; mr1023 (Ind_All); LR P-value: 6.20E-09; mr1044 (All); LR P-value: 1.87E-07; mr1044 (Ind_All); LR P-value: 1.00E-06; mr1055 (Ind_All); LR P-value: 7.00E-12; mr1079 (Ind_All); LR P-value: 1.21E-14; mr1132 (Ind_All); LR P-value: 4.02E-10; mr1142 (Ind_All); LR P-value: 6.16E-11; mr1178 (Ind_All); LR P-value: 9.10E-16; mr1301 (Ind_All); LR P-value: 7.49E-09; mr1352 (Ind_All); LR P-value: 6.81E-06; mr1390 (Ind_All); LR P-value: 4.16E-14; mr1489 (Ind_All); LR P-value: 5.99E-08; mr1490 (Ind_All); LR P-value: 1.68E-14; mr1491 (Ind_All); LR P-value: 5.65E-11; mr1546 (Ind_All); LR P-value: 7.68E-09; mr1115_2 (Ind_All); LR P-value: 5.70E-07; mr1132_2 (Ind_All); LR P-value: 3.79E-12; mr1141_2 (Ind_All); LR P-value: 7.28E-11; mr1178_2 (Ind_All); LR P-value: 6.70E-13; mr1193_2 (Ind_All); LR P-value: 4.42E-06; mr1195_2 (Ind_All); LR P-value: 8.40E-15; mr1235_2 (Ind_All); LR P-value: 7.69E-08; mr1241_2 (Ind_All); LR P-value: 2.86E-08; mr1352_2 (Ind_All); LR P-value: 3.54E-10; mr1390_2 (Ind_All); LR P-value: 2.08E-12; mr1402_2 (Ind_All); LR P-value: 7.37E-06; mr1482_2 (Ind_All); LR P-value: 1.14E-07; mr1490_2 (Ind_All); LR P-value: 2.46E-12; mr1546_2 (Ind_All); LR P-value: 6.65E-10; mr1580_2 (Ind_All); LR P-value: 3.39E-06; mr1611_2 (Ind_All); LR P-value: 9.25E-06; mr1624_2 (Ind_All); LR P-value: 9.98E-06; mr1682_2 (Ind_All); LR P-value: 1.25E-07; mr1798_2 (Jap_All); LR P-value: 4.73E-07; mr1825_2 (Ind_All); LR P-value: 3.48E-06; mr1828_2 (Ind_All); LMM P-value: 1.73E-07; LR P-value: 2.62E-12; mr1938_2 (Ind_All); LR P-value: 2.96E-07 |
LOC_Os05g47520.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 93.485; most accessible tissue: Zhenshan97 flower, score: 96.805 |
| vg0527223548 (J) | chr05 | 27223548 | GTCGTCA | G | 89.10% | 0.06% | GTCGTCA -> G | NA |
LOC_Os05g47520.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g47520.1 Alt: G| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 94.432; most accessible tissue: Zhenshan97 flower, score: 97.933 |
| vg0527223554 (J) | chr05 | 27223554 | G | A | 68.80% | 0.00% | A -> G |
mr1115 (All); LR P-value: 4.50E-22;
mr1300 (All); LR P-value: 7.57E-22; mr1448 (Jap_All); LR P-value: 8.71E-06; mr1611 (All); LR P-value: 1.42E-22; mr1611 (Jap_All); LR P-value: 7.62E-13; mr1629 (Jap_All); LR P-value: 9.15E-07; mr1920 (All); LR P-value: 5.26E-23; mr1920 (Jap_All); LR P-value: 1.51E-11; mr1926 (All); LR P-value: 3.58E-40; mr1156_2 (All); LR P-value: 9.28E-18; mr1156_2 (Jap_All); LR P-value: 6.52E-08; mr1189_2 (Jap_All); LR P-value: 3.72E-09; mr1310_2 (All); LR P-value: 2.25E-32; mr1361_2 (All); LR P-value: 1.23E-20; mr1364_2 (All); LR P-value: 1.85E-08; mr1364_2 (Jap_All); LR P-value: 8.88E-10; mr1383_2 (Jap_All); LR P-value: 1.85E-06; mr1454_2 (Jap_All); LR P-value: 4.27E-10; mr1471_2 (All); LR P-value: 1.09E-08; mr1471_2 (Jap_All); LR P-value: 2.18E-10; mr1530_2 (Jap_All); LR P-value: 5.34E-10; mr1580_2 (Jap_All); LR P-value: 2.01E-10; mr1642_2 (Jap_All); LR P-value: 2.43E-09; mr1825_2 (Jap_All); LR P-value: 6.70E-10; mr1879_2 (All); LR P-value: 4.49E-11; mr1879_2 (Jap_All); LR P-value: 4.57E-08; mr1959_2 (All); LR P-value: 7.55E-14; mr1980_2 (All); LR P-value: 5.41E-18 |
LOC_Os05g47520.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 94.594; most accessible tissue: Zhenshan97 flower, score: 98.128 |
| vg0527223564 (J) | chr05 | 27223564 | T | G | 96.40% | 0.00% | T -> G | NA |
LOC_Os05g47520.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 95.249; most accessible tissue: Zhenshan97 flower, score: 98.410 |
| vg0527223567 (J) | chr05 | 27223567 | T | G | 53.00% | 0.02% | T -> G | NA |
LOC_Os05g47520.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g47520.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 95.242; most accessible tissue: Zhenshan97 flower, score: 98.413 |