13 variations found. Os04g0504700/LOC_Os04g42590 (expressed protein), ranging from 25,191,053 bp to 25,192,947 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os04g42590 | expressed protein; RAP ID: Os04g0504700; MSU ID: LOC_Os04g42590 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0425191270 (J) | chr04 | 25191270 | G | C | 51.00% | 0.30% | G -> C |
mr1026 (All); LR P-value: 6.26E-34;
mr1063 (All); LR P-value: 2.97E-52; mr1091 (All); LR P-value: 2.93E-39; mr1094 (All); LR P-value: 3.20E-39; mr1096 (All); LR P-value: 3.87E-51; mr1110 (All); LR P-value: 9.25E-39; mr1112 (All); LR P-value: 3.46E-44; mr1161 (All); LR P-value: 2.43E-34; mr1183 (All); LR P-value: 1.91E-13; mr1237 (All); LR P-value: 6.02E-30; mr1261 (All); LR P-value: 1.18E-16; mr1352 (All); LR P-value: 1.51E-10; mr1457 (All); LR P-value: 9.07E-09; mr1458 (All); LR P-value: 1.66E-43; mr1503 (All); LR P-value: 2.30E-13; mr1798 (All); LR P-value: 3.69E-50; mr1870 (All); LR P-value: 1.37E-15; mr1873 (Ind_All); LR P-value: 2.46E-06; mr1914 (All); LR P-value: 1.93E-12; mr1063_2 (All); LR P-value: 8.95E-54; mr1091_2 (All); LR P-value: 5.79E-51; mr1094_2 (All); LR P-value: 1.68E-47; mr1110_2 (All); LR P-value: 6.34E-38; mr1161_2 (All); LR P-value: 5.17E-35; mr1164_2 (All); LR P-value: 1.12E-21; mr1180_2 (All); LR P-value: 2.39E-16; mr1183_2 (All); LR P-value: 5.12E-21; mr1218_2 (All); LR P-value: 3.74E-19; mr1220_2 (All); LR P-value: 3.54E-10; mr1221_2 (All); LR P-value: 3.28E-38; mr1260_2 (All); LR P-value: 1.58E-16; mr1422_2 (All); LR P-value: 1.77E-23; mr1457_2 (All); LR P-value: 7.53E-17; mr1458_2 (All); LR P-value: 1.03E-46; mr1579_2 (All); LR P-value: 1.75E-14; mr1579_2 (Ind_All); LR P-value: 8.03E-06; mr1751_2 (All); LR P-value: 1.02E-09; mr1798_2 (All); LR P-value: 1.41E-67; mr1870_2 (All); LR P-value: 1.97E-20; mr1873_2 (Ind_All); LR P-value: 1.97E-06 |
LOC_Os04g42580.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g42590.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g42570.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g42600.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g42600.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 75.870; most accessible tissue: Minghui63 flag leaf, score: 93.371 |
| vg0425191273 (J) | chr04 | 25191273 | G | C | 89.00% | 0.00% | G -> C |
LOC_Os04g42580.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g42590.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g42570.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g42600.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g42600.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.072; most accessible tissue: Minghui63 flag leaf, score: 93.280 |
|
| vg0425191540 (J) | chr04 | 25191540 | A | AT | 51.00% | 0.00% | A -> AT | NA |
LOC_Os04g42580.1 Alt: AT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g42590.1 Alt: AT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g42570.1 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g42600.1 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g42600.2 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 87.408; most accessible tissue: Callus, score: 96.728 |
| vg0425191598 (J) | chr04 | 25191598 | C | A | 54.50% | 0.38% | A -> C |
mr1873 (Ind_All); LR P-value: 3.80E-07;
mr1302_2 (All); LR P-value: 2.48E-07; mr1488_2 (All); LR P-value: 4.66E-07; mr1521_2 (All); LR P-value: 3.42E-13; mr1579_2 (All); LR P-value: 1.31E-15; mr1579_2 (Ind_All); LR P-value: 2.81E-06; mr1580_2 (All); LR P-value: 1.74E-29; mr1604_2 (All); LR P-value: 6.94E-08; mr1653_2 (Ind_All); LR P-value: 7.14E-07; mr1683_2 (All); LR P-value: 1.84E-07; mr1759_2 (Ind_All); LR P-value: 3.12E-06; mr1800_2 (Ind_All); LR P-value: 6.68E-06; mr1824_2 (All); LR P-value: 1.07E-07; mr1838_2 (All); LR P-value: 4.76E-13; mr1873_2 (All); LR P-value: 3.70E-32; mr1873_2 (Ind_All); LR P-value: 2.02E-06; mr1922_2 (All); LR P-value: 1.74E-19 |
LOC_Os04g42580.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g42590.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g42570.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g42600.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g42600.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 88.058; most accessible tissue: Minghui63 flag leaf, score: 94.364 |
| vg0425191611 (J) | chr04 | 25191611 | C | T | 50.90% | 0.36% | C -> T |
mr1026 (All); LR P-value: 3.97E-35;
mr1059 (Ind_All); LR P-value: 1.90E-07; mr1063 (All); LR P-value: 9.73E-53; mr1091 (All); LR P-value: 1.08E-38; mr1094 (All); LR P-value: 6.11E-40; mr1096 (All); LR P-value: 1.54E-49; mr1110 (All); LR P-value: 2.62E-37; mr1161 (All); LR P-value: 1.71E-35; mr1183 (All); LR P-value: 3.97E-14; mr1260 (All); LR P-value: 4.07E-08; mr1261 (All); LR P-value: 2.37E-16; mr1352 (All); LR P-value: 4.25E-10; mr1458 (All); LR P-value: 6.39E-43; mr1503 (All); LR P-value: 6.34E-14; mr1798 (All); LR P-value: 7.72E-50; mr1870 (All); LR P-value: 6.37E-16; mr1873 (Ind_All); LR P-value: 2.03E-07; mr1914 (All); LR P-value: 6.46E-13; mr1063_2 (All); LR P-value: 4.69E-55; mr1091_2 (All); LR P-value: 5.90E-49; mr1094_2 (All); LR P-value: 9.94E-47; mr1161_2 (All); LR P-value: 1.36E-35; mr1164_2 (All); LR P-value: 6.35E-22; mr1180_2 (All); LR P-value: 3.94E-17; mr1183_2 (All); LR P-value: 9.64E-22; mr1218_2 (All); LR P-value: 8.51E-19; mr1220_2 (All); LR P-value: 3.65E-10; mr1221_2 (All); LR P-value: 2.21E-37; mr1260_2 (All); LR P-value: 5.75E-17; mr1422_2 (All); LR P-value: 4.42E-23; mr1457_2 (All); LR P-value: 2.56E-16; mr1488_2 (All); LR P-value: 1.91E-06; mr1579_2 (All); LR P-value: 5.28E-15; mr1579_2 (Ind_All); LR P-value: 2.50E-06; mr1751_2 (All); LR P-value: 4.49E-10; mr1798_2 (All); LR P-value: 4.68E-68; mr1824_2 (All); LR P-value: 4.29E-07; mr1870_2 (All); LR P-value: 2.10E-20; mr1873_2 (Ind_All); LR P-value: 6.99E-07 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g42580.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g42590.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g42570.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g42600.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g42600.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 87.762; most accessible tissue: Minghui63 flag leaf, score: 94.221 |
| vg0425191874 (J) | chr04 | 25191874 | A | ATGGCAT CTGTGAT CT | 53.40% | 0.40% | A -> ATGGCATCTG TGATCT | NA |
LOC_Os04g42590.1 Alt: ATGGCATCTGTGATCT| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os04g42590.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 90.180; most accessible tissue: Minghui63 flag leaf, score: 95.707 |
| vg0425192250 (J) | chr04 | 25192250 | C | G | 98.10% | 0.00% | C -> G | NA |
LOC_Os04g42590.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 88.902; most accessible tissue: Minghui63 flag leaf, score: 95.963 |
| vg0425192355 (J) | chr04 | 25192355 | C | A | 64.30% | 0.00% | C -> A |
mr1026 (All); LR P-value: 4.88E-35;
mr1161 (All); LR P-value: 6.90E-36; mr1610 (All); LR P-value: 8.27E-08; mr1798 (All); LR P-value: 2.11E-48; mr1798 (Ind_All); LR P-value: 9.87E-07; mr1870 (All); LR P-value: 3.67E-16; mr1914 (All); LR P-value: 1.33E-12; mr1172_2 (All); LR P-value: 1.16E-08; mr1870_2 (All); LR P-value: 8.62E-20; mr1870_2 (Ind_All); LR P-value: 4.17E-06 |
LOC_Os04g42590.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 88.170; most accessible tissue: Minghui63 flag leaf, score: 97.346 |
| vg0425192447 (J) | chr04 | 25192447 | C | T | 58.40% | 0.00% | C -> T |
LOC_Os04g42590.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 92.642; most accessible tissue: Minghui63 flag leaf, score: 98.078 |
|
| vg0425192464 (J) | chr04 | 25192464 | C | T | 94.90% | 1.25% | C -> T | NA |
LOC_Os04g42590.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g42590.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 92.642; most accessible tissue: Minghui63 flag leaf, score: 98.105 |
| vg0425192708 (J) | chr04 | 25192708 | A | C | 94.30% | 0.00% | A -> C | NA |
LOC_Os04g42580.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g42600.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g42600.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g42590.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 93.153; most accessible tissue: Minghui63 flag leaf, score: 98.022 |
| vg0425192788 (J) | chr04 | 25192788 | C | T | 64.30% | 0.76% | C -> T |
mr1026 (All); LR P-value: 9.13E-36;
mr1063 (Ind_All); LR P-value: 6.17E-06; mr1161 (All); LR P-value: 1.10E-36; mr1237 (All); LR P-value: 4.03E-29; mr1261 (All); LR P-value: 2.60E-14; mr1352 (All); LR P-value: 2.72E-09; mr1610 (All); LR P-value: 3.72E-08; mr1798 (All); LR P-value: 4.00E-50; mr1798 (Ind_All); LR P-value: 8.28E-07; mr1870 (All); LR P-value: 1.07E-16; mr1914 (All); LR P-value: 1.34E-12; mr1172_2 (All); LR P-value: 1.17E-08; mr1870_2 (All); LR P-value: 1.43E-20; mr1870_2 (Ind_All); LR P-value: 1.70E-06 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g42590.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g42580.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g42600.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g42600.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 94.192; most accessible tissue: Minghui63 flag leaf, score: 98.604 |
| STR0425191268 (J) | chr04 | 25191268 | TTCTTG | TTCTTC | 47.70% | 0.00% | TTGTTG -> TTCTTC,TTC TTG | NA |
|