15 variations found. Os01g0750400/LOC_Os01g54630 (leucine rich repeat family protein; putative; expressed), ranging from 31,431,622 bp to 31,433,202 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os01g54630 | leucine rich repeat family protein, putative, expressed; RAP ID: Os01g0750400; MSU ID: LOC_Os01g54630 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0131431638 (J) | chr01 | 31431638 | A | T | 67.40% | 0.00% | T -> A |
mr1003 (All); LR P-value: 1.35E-22;
mr1008 (All); LR P-value: 1.02E-105; mr1009 (All); LR P-value: 5.47E-105; mr1010 (All); LR P-value: 2.88E-13; mr1163 (All); LR P-value: 1.54E-21; mr1239 (All); LR P-value: 6.60E-14; mr1242 (All); LR P-value: 3.96E-20; mr1781 (All); LR P-value: 3.39E-07; mr1010_2 (All); LR P-value: 3.52E-21; mr1051_2 (All); LR P-value: 5.64E-27; mr1114_2 (All); LR P-value: 2.53E-16; mr1118_2 (All); LR P-value: 1.01E-14; mr1242_2 (All); LR P-value: 6.04E-24; mr1496_2 (All); LR P-value: 3.52E-15; mr1645_2 (All); LR P-value: 5.78E-08; mr1700_2 (All); LR P-value: 2.13E-08; mr1781_2 (All); LR P-value: 5.38E-11; mr1840_2 (All); LR P-value: 6.39E-06 |
LOC_Os01g54630.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g54620.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g54640.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 73.145; most accessible tissue: Zhenshan97 panicle, score: 93.752 |
| vg0131431837 (J) | chr01 | 31431837 | A | G | 87.50% | 0.00% | A -> G | NA |
LOC_Os01g54630.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g54620.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g54640.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 77.761; most accessible tissue: Zhenshan97 panicle, score: 93.752 |
| vg0131431842 (J) | chr01 | 31431842 | C | T | 99.00% | 0.00% | C -> T | NA |
LOC_Os01g54630.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g54620.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g54640.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 77.753; most accessible tissue: Zhenshan97 panicle, score: 93.936 |
| vg0131431925 (J) | chr01 | 31431925 | G | A | 99.00% | 0.00% | G -> A | NA |
LOC_Os01g54630.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os01g54620.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g54640.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 80.155; most accessible tissue: Zhenshan97 panicle, score: 92.784 |
| vg0131432101 (J) | chr01 | 31432101 | G | GCGCCGT | 66.90% | 0.00% | GCGCCGT -> G | NA |
LOC_Os01g54630.1 Alt: G| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 82.230; most accessible tissue: Zhenshan97 panicle, score: 94.360 |
| vg0131432613 (J) | chr01 | 31432613 | A | C | 64.00% | 0.00% | C -> A | NA |
LOC_Os01g54630.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 87.777; most accessible tissue: Zhenshan97 panicle, score: 95.323 |
| vg0131432651 (J) | chr01 | 31432651 | G | A | 90.60% | 0.00% | G -> A |
mr1240 (All); LR P-value: 8.55E-17;
mr1530 (All); LR P-value: 3.84E-07; mr1858 (All); LR P-value: 3.20E-28; mr1859 (All); LR P-value: 2.95E-28; mr1897 (All); LR P-value: 6.01E-12; mr1098_2 (All); LR P-value: 6.53E-32; mr1099_2 (All); LR P-value: 3.92E-23; mr1123_2 (All); LR P-value: 5.63E-23; mr1240_2 (All); LR P-value: 9.55E-20; mr1918_2 (All); LR P-value: 2.72E-14; mr1936_2 (All); LR P-value: 8.42E-16 |
LOC_Os01g54630.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 87.414; most accessible tissue: Zhenshan97 panicle, score: 94.949 |
| vg0131432655 (J) | chr01 | 31432655 | G | A | 99.00% | 0.00% | G -> A | NA |
LOC_Os01g54630.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 87.517; most accessible tissue: Zhenshan97 panicle, score: 95.016 |
| vg0131432734 (J) | chr01 | 31432734 | C | A | 68.20% | 0.00% | C -> A |
Plant_height (All); LR P-value: 3.21E-19;
Plant_height (Ind_All); LR P-value: 1.35E-16; mr1003 (All); LR P-value: 4.24E-25; mr1003 (Ind_All); LR P-value: 3.64E-07; mr1011 (All); LR P-value: 3.25E-06; mr1013 (All); LR P-value: 8.92E-15; mr1013 (Ind_All); LR P-value: 3.24E-06; mr1031 (All); LR P-value: 9.23E-15; mr1031 (Ind_All); LR P-value: 8.97E-07; mr1034 (All); LR P-value: 1.62E-12; mr1034 (Ind_All); LR P-value: 4.21E-06; mr1042 (Ind_All); LR P-value: 2.66E-06; mr1043 (Ind_All); LR P-value: 1.01E-06; mr1051 (All); LR P-value: 1.05E-25; mr1051 (Ind_All); LR P-value: 2.91E-07; mr1056 (All); LR P-value: 1.24E-13; mr1201 (Ind_All); LR P-value: 3.19E-06; mr1219 (Ind_All); LR P-value: 3.71E-06; mr1677 (Ind_All); LR P-value: 1.71E-06; mr1912 (Ind_All); LR P-value: 6.48E-06; mr1060_2 (Ind_All); LR P-value: 3.70E-06; mr1084_2 (All); LR P-value: 4.00E-08; mr1115_2 (Ind_All); LR P-value: 2.23E-07; mr1174_2 (All); LR P-value: 3.57E-11; mr1180_2 (All); LR P-value: 1.92E-15; mr1183_2 (All); LR P-value: 3.79E-22; mr1207_2 (Ind_All); LR P-value: 9.72E-06; mr1215_2 (All); LR P-value: 1.00E-09; mr1260_2 (All); LR P-value: 9.55E-19; mr1268_2 (Ind_All); LR P-value: 2.00E-06; mr1274_2 (Ind_All); LR P-value: 2.34E-07; mr1302_2 (All); LR P-value: 2.29E-08; mr1306_2 (Ind_All); LR P-value: 3.67E-06; mr1319_2 (All); LR P-value: 3.49E-10; mr1327_2 (All); LR P-value: 2.48E-09; mr1327_2 (Ind_All); LR P-value: 8.73E-10; mr1330_2 (All); LR P-value: 1.33E-14; mr1330_2 (Ind_All); LR P-value: 1.32E-06; mr1352_2 (All); LR P-value: 3.64E-23; mr1352_2 (Ind_All); LR P-value: 1.25E-10; mr1376_2 (All); LR P-value: 3.26E-09; mr1422_2 (All); LR P-value: 1.69E-24; mr1428_2 (All); LR P-value: 8.46E-07; mr1431_2 (All); LR P-value: 9.19E-10; mr1565_2 (All); LR P-value: 7.27E-12; mr1565_2 (Ind_All); LR P-value: 1.01E-09; mr1611_2 (Ind_All); LR P-value: 1.95E-06; mr1624_2 (Ind_All); LR P-value: 3.91E-08; mr1653_2 (Ind_All); LR P-value: 2.84E-07; mr1681_2 (All); LR P-value: 1.75E-08; mr1681_2 (Ind_All); LR P-value: 8.67E-06; mr1696_2 (Ind_All); LR P-value: 8.54E-06; mr1735_2 (Ind_All); LR P-value: 9.23E-06; mr1739_2 (Ind_All); LR P-value: 2.51E-09; mr1751_2 (All); LR P-value: 1.42E-08; mr1758_2 (Ind_All); LR P-value: 6.84E-10; mr1771_2 (Ind_All); LR P-value: 1.31E-06; mr1784_2 (Ind_All); LR P-value: 7.03E-06; mr1824_2 (All); LR P-value: 2.80E-07; mr1885_2 (All); LR P-value: 3.61E-07; mr1959_2 (Ind_All); LR P-value: 3.92E-06 |
LOC_Os01g54630.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 90.196; most accessible tissue: Zhenshan97 panicle, score: 95.951 |
| vg0131432852 (J) | chr01 | 31432852 | C | T | 99.00% | 0.00% | C -> T | NA |
LOC_Os01g54630.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 87.704; most accessible tissue: Zhenshan97 panicle, score: 95.855 |
| vg0131433010 (J) | chr01 | 31433010 | C | T | 89.10% | 4.02% | C -> T | NA |
LOC_Os01g54630.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g54630.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 91.639; most accessible tissue: Zhenshan97 panicle, score: 97.556 |
| vg0131433018 (J) | chr01 | 31433018 | C | T | 89.20% | 3.89% | C -> T | NA |
LOC_Os01g54630.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g54630.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 91.591; most accessible tissue: Zhenshan97 panicle, score: 97.641 |
| vg0131433146 (J) | chr01 | 31433146 | T | C | 99.70% | 0.00% | T -> C | NA |
LOC_Os01g54630.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 95.118; most accessible tissue: Zhenshan97 panicle, score: 99.328 |
| vg0131433190 (J) | chr01 | 31433190 | T | C | 87.50% | 0.00% | T -> C | NA |
LOC_Os01g54630.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 97.242; most accessible tissue: Zhenshan97 panicle, score: 99.519 |
| STR0131432102 (J) | chr01 | 31432102 | C | CGCCGTC | 60.70% | 0.00% | CGCCGTC -> C | NA |
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