2 variations found. Os01g0736600/LOC_Os01g53500 (RING-H2 finger protein ATL2M; putative; expressed), ranging from 30,730,644 bp to 30,731,238 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os01g53500 | RING-H2 finger protein ATL2M, putative, expressed; RAP ID: Os01g0736600; MSU ID: LOC_Os01g53500 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0130730796 (J) | chr01 | 30730796 | CA | GA | 57.10% | 0.61% | CA -> GA,C |
mr1013 (All); LR P-value: 5.48E-13;
mr1031 (All); LR P-value: 2.76E-13; mr1031 (Ind_All); LR P-value: 6.59E-06; mr1034 (All); LR P-value: 2.89E-12; mr1051 (All); LR P-value: 2.03E-21; mr1056 (All); LR P-value: 8.87E-13; mr1174 (All); LR P-value: 3.72E-09; mr1183 (All); LR P-value: 6.84E-13; mr1219 (Ind_All); LR P-value: 3.01E-06; mr1552 (All); LR P-value: 1.87E-18; mr1045_2 (Ind_All); LR P-value: 9.06E-06; mr1084_2 (All); LR P-value: 9.98E-09; mr1169_2 (Ind_All); LR P-value: 9.38E-07; mr1172_2 (All); LR P-value: 1.38E-08; mr1174_2 (All); LR P-value: 4.46E-15; mr1174_2 (Ind_All); LR P-value: 1.74E-09; mr1180_2 (All); LR P-value: 2.99E-16; mr1183_2 (All); LR P-value: 2.99E-23; mr1215_2 (All); LR P-value: 1.68E-07; mr1260_2 (All); LR P-value: 8.43E-17; mr1268_2 (Ind_All); LR P-value: 1.49E-06; mr1274_2 (Ind_All); LR P-value: 8.49E-07; mr1302_2 (All); LR P-value: 4.57E-07; mr1330_2 (All); LR P-value: 6.80E-13; mr1347_2 (All); LR P-value: 2.65E-08; mr1347_2 (Ind_All); LR P-value: 4.51E-07; mr1352_2 (All); LR P-value: 1.26E-16; mr1376_2 (All); LR P-value: 4.08E-08; mr1431_2 (All); LR P-value: 1.05E-08; mr1521_2 (All); LR P-value: 6.86E-14; mr1565_2 (All); LR P-value: 1.62E-10; mr1627_2 (All); LR P-value: 1.60E-20; mr1681_2 (All); LR P-value: 4.88E-08; mr1696_2 (Ind_All); LR P-value: 2.67E-06; mr1751_2 (All); LR P-value: 1.01E-08; mr1758_2 (Ind_All); LR P-value: 2.44E-10; mr1885_2 (All); LR P-value: 1.51E-07 |
LOC_Os01g53500.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g53500.1 Alt: C| frameshift_variant HIGH(snpEff) LOC_Os01g53500.1 Alt: GA/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 90.708; most accessible tissue: Zhenshan97 flower, score: 93.944 |
| vg0130730893 (J) | chr01 | 30730893 | C | A | 57.10% | 0.36% | C -> A |
mr1013 (All); LR P-value: 1.17E-13;
mr1031 (All); LR P-value: 1.27E-13; mr1031 (Ind_All); LR P-value: 5.01E-06; mr1051 (All); LR P-value: 1.59E-21; mr1056 (All); LR P-value: 3.54E-13; mr1174 (All); LR P-value: 2.23E-09; mr1183 (All); LR P-value: 6.88E-14; mr1255 (All); LR P-value: 7.58E-18; mr1503 (All); LR P-value: 3.46E-13; mr1552 (All); LR P-value: 7.42E-19; mr1913 (All); LR P-value: 1.42E-17; mr1918 (Ind_All); LR P-value: 7.86E-06; mr1929 (All); LR P-value: 2.25E-08; mr1045_2 (Ind_All); LR P-value: 3.22E-06; mr1084_2 (All); LR P-value: 1.15E-08; mr1169_2 (Ind_All); LR P-value: 9.91E-07; mr1172_2 (All); LR P-value: 2.44E-09; mr1174_2 (All); LR P-value: 1.29E-13; mr1174_2 (Ind_All); LR P-value: 9.09E-10; mr1180_2 (All); LR P-value: 9.06E-18; mr1183_2 (All); LR P-value: 6.18E-25; mr1183_2 (Ind_All); LR P-value: 3.18E-07; mr1215_2 (All); LR P-value: 7.76E-08; mr1260_2 (All); LR P-value: 4.75E-17; mr1268_2 (Ind_All); LR P-value: 6.70E-07; mr1274_2 (Ind_All); LR P-value: 8.38E-07; mr1302_2 (All); LR P-value: 8.15E-08; mr1330_2 (All); LR P-value: 7.00E-13; mr1347_2 (All); LR P-value: 4.19E-08; mr1347_2 (Ind_All); LR P-value: 1.11E-07; mr1352_2 (All); LR P-value: 6.09E-18; mr1376_2 (All); LR P-value: 5.18E-08; mr1431_2 (All); LR P-value: 1.41E-08; mr1521_2 (All); LR P-value: 1.01E-13; mr1565_2 (All); LR P-value: 8.13E-11; mr1604_2 (All); LR P-value: 4.24E-07; mr1681_2 (All); LR P-value: 2.71E-08; mr1696_2 (Ind_All); LR P-value: 4.37E-06; mr1735_2 (Ind_All); LR P-value: 6.79E-06; mr1751_2 (All); LR P-value: 4.24E-09; mr1758_2 (Ind_All); LR P-value: 6.51E-09; mr1824_2 (All); LR P-value: 3.09E-07; mr1885_2 (All); LR P-value: 4.78E-08 |
LOC_Os01g53500.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g53500.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 88.149; most accessible tissue: Zhenshan97 flower, score: 94.783 |