18 variations found. Os07g0145400/LOC_Os07g05190 (leucine-rich repeat family protein; putative; expressed), ranging from 2,313,395 bp to 2,319,009 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os07g05190 | leucine-rich repeat family protein, putative, expressed; RAP ID: Os07g0145400; MSU ID: LOC_Os07g05190 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0702313507 (J) | chr07 | 2313507 | C | A | 99.90% | 0.00% | C -> A | NA |
LOC_Os07g05190.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os07g05180.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 67.158; most accessible tissue: Zhenshan97 panicle, score: 94.026 |
| vg0702313558 (J) | chr07 | 2313558 | T | C | 57.70% | 0.28% | C -> T |
mr1004 (All); LR P-value: 1.44E-06;
mr1005 (All); LR P-value: 1.17E-11; mr1146 (All); LR P-value: 2.53E-14; mr1150 (All); LR P-value: 7.77E-22; mr1874 (All); LR P-value: 3.57E-14; mr1950 (All); LR P-value: 5.37E-15; mr1158_2 (Ind_All); LR P-value: 5.49E-10; mr1383_2 (Ind_All); LR P-value: 6.19E-11; mr1520_2 (All); LR P-value: 2.10E-11; mr1645_2 (All); LR P-value: 9.59E-08; mr1654_2 (All); LR P-value: 2.67E-07; mr1874_2 (All); LR P-value: 1.31E-18 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g05190.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g05180.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 66.210; most accessible tissue: Zhenshan97 panicle, score: 94.594 |
| vg0702313588 (J) | chr07 | 2313588 | C | T | 93.70% | 0.00% | C -> T |
mr1006 (All); LR P-value: 4.91E-06;
mr1028 (All); LR P-value: 2.87E-06; mr1030 (All); LR P-value: 7.40E-06; mr1058 (All); LR P-value: 1.65E-06; mr1073 (All); LR P-value: 4.33E-08; mr1095 (All); LR P-value: 1.93E-26; mr1098 (All); LR P-value: 1.77E-38; mr1099 (All); LR P-value: 1.40E-34; mr1101 (All); LR P-value: 4.35E-32; mr1113 (All); LR P-value: 5.94E-16; mr1114 (All); LR P-value: 1.42E-18; mr1117 (All); LR P-value: 4.22E-21; mr1119 (All); LR P-value: 4.60E-17; mr1120 (All); LR P-value: 8.00E-24; mr1123 (All); LR P-value: 3.18E-28; mr1126 (All); LR P-value: 2.32E-06; mr1146 (All); LR P-value: 1.68E-15; mr1153 (All); LR P-value: 3.43E-06; mr1158 (All); LR P-value: 2.74E-15; mr1168 (All); LR P-value: 1.51E-21; mr1210 (All); LR P-value: 2.04E-22; mr1230 (All); LR P-value: 1.08E-07; mr1231 (All); LR P-value: 3.44E-13; mr1240 (All); LR P-value: 7.90E-19; mr1247 (All); LR P-value: 3.94E-24; mr1262 (All); LR P-value: 2.17E-06; mr1305 (All); LR P-value: 1.14E-25; mr1331 (All); LR P-value: 3.97E-06; mr1345 (All); LR P-value: 4.63E-07; mr1348 (All); LR P-value: 3.24E-08; mr1365 (All); LR P-value: 6.97E-09; mr1367 (All); LR P-value: 6.50E-06; mr1382 (All); LR P-value: 7.03E-07; mr1393 (All); LR P-value: 2.96E-06; mr1409 (All); LR P-value: 2.65E-12; mr1417 (All); LR P-value: 9.55E-06; mr1424 (All); LR P-value: 7.73E-06; mr1427 (All); LR P-value: 2.17E-06; mr1442 (All); LR P-value: 9.31E-09; mr1453 (All); LR P-value: 5.73E-07; mr1496 (All); LR P-value: 1.30E-14; mr1499 (All); LR P-value: 4.48E-12; mr1512 (All); LR P-value: 7.09E-06; mr1515 (All); LR P-value: 4.17E-20; mr1522 (All); LR P-value: 8.63E-12; mr1523 (All); LR P-value: 3.12E-06; mr1545 (All); LR P-value: 8.50E-06; mr1549 (All); LR P-value: 4.88E-41; mr1550 (All); LMM P-value: 3.41E-06; LR P-value: 1.09E-47; mr1574 (All); LR P-value: 4.35E-06; mr1586 (All); LR P-value: 1.12E-28; mr1589 (All); LR P-value: 5.89E-28; mr1612 (All); LR P-value: 9.93E-13; mr1621 (All); LR P-value: 6.94E-07; mr1634 (All); LR P-value: 1.08E-07; mr1649 (All); LR P-value: 9.64E-14; mr1665 (All); LR P-value: 1.95E-06; mr1696 (All); LR P-value: 1.86E-11; mr1727 (All); LR P-value: 8.73E-06; mr1730 (All); LR P-value: 1.81E-09; mr1757 (All); LR P-value: 2.82E-42; mr1762 (All); LR P-value: 6.48E-07; mr1765 (All); LR P-value: 3.12E-18; mr1774 (All); LR P-value: 2.97E-06; mr1858 (All); LR P-value: 2.35E-29; mr1859 (All); LR P-value: 2.13E-29; mr1866 (All); LR P-value: 1.01E-08; mr1868 (All); LR P-value: 1.18E-29; mr1911 (All); LR P-value: 2.95E-18; mr1918 (All); LR P-value: 3.13E-13; mr1931 (All); LR P-value: 9.18E-07; mr1936 (All); LR P-value: 2.09E-18; mr1939 (All); LR P-value: 5.71E-09; mr1942 (All); LR P-value: 1.24E-07; mr1961 (All); LR P-value: 4.25E-23; mr1047_2 (All); LR P-value: 4.87E-12; mr1095_2 (All); LR P-value: 1.51E-21; mr1098_2 (All); LR P-value: 9.31E-35; mr1099_2 (All); LR P-value: 5.51E-27; mr1123_2 (All); LR P-value: 5.27E-21; mr1305_2 (All); LR P-value: 1.43E-20; mr1409_2 (All); LR P-value: 1.08E-12; mr1510_2 (All); LR P-value: 3.23E-09; mr1549_2 (All); LR P-value: 1.82E-33; mr1550_2 (All); LR P-value: 2.71E-46; mr1740_2 (All); LR P-value: 3.84E-06; mr1741_2 (All); LR P-value: 5.95E-09; mr1757_2 (All); LR P-value: 2.37E-26; mr1792_2 (All); LR P-value: 3.31E-07; mr1803_2 (All); LR P-value: 5.91E-15; mr1808_2 (All); LR P-value: 5.11E-07; mr1815_2 (All); LR P-value: 1.65E-06; mr1911_2 (All); LR P-value: 1.54E-15 |
LOC_Os07g05190.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g05180.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 62.985; most accessible tissue: Zhenshan97 panicle, score: 94.195 |
| vg0702314188 (J) | chr07 | 2314188 | G | A | 99.40% | 0.00% | G -> A | NA |
LOC_Os07g05190.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 74.817; most accessible tissue: Zhenshan97 panicle, score: 94.278 |
| vg0702314200 (J) | chr07 | 2314200 | G | A | 50.70% | 0.32% | A -> G,T |
mr1216 (All); LR P-value: 4.61E-06;
mr1158_2 (All); LR P-value: 1.07E-06; mr1158_2 (Ind_All); LR P-value: 2.19E-12; mr1383_2 (Ind_All); LR P-value: 2.66E-12; mr1478_2 (All); LR P-value: 1.91E-09; mr1608_2 (Ind_All); LR P-value: 2.87E-06; mr1648_2 (All); LR P-value: 4.16E-06; mr1971_2 (All); LR P-value: 3.24E-22 |
LOC_Os07g05190.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g05190.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os07g05190.1 Alt: T| synonymous_variant LOW(snpEff) LOC_Os07g05180.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 75.507; most accessible tissue: Zhenshan97 panicle, score: 94.360 |
| vg0702314591 (J) | chr07 | 2314591 | C | T | 57.80% | 0.25% | T -> C |
mr1004 (All); LR P-value: 2.12E-06;
mr1005 (All); LR P-value: 2.47E-11; mr1146 (All); LR P-value: 2.07E-14; mr1150 (All); LR P-value: 6.68E-22; mr1874 (All); LR P-value: 4.12E-14; mr1158_2 (Ind_All); LR P-value: 1.22E-09; mr1195_2 (All); LR P-value: 1.60E-18; mr1383_2 (Ind_All); LR P-value: 7.80E-12; mr1520_2 (All); LR P-value: 1.73E-11; mr1645_2 (All); LR P-value: 4.29E-08; mr1654_2 (All); LR P-value: 2.31E-07; mr1874_2 (All); LR P-value: 7.09E-19 |
LOC_Os07g05190.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g05190.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 62.236; most accessible tissue: Zhenshan97 panicle, score: 83.904 |
| vg0702314970 (J) | chr07 | 2314970 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os07g05190.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os07g05180.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 63.711; most accessible tissue: Zhenshan97 panicle, score: 87.451 |
| vg0702315611 (J) | chr07 | 2315611 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os07g05190.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os07g05180.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 41.683; most accessible tissue: Zhenshan97 young leaf, score: 60.208 |
| vg0702315769 (J) | chr07 | 2315769 | C | T | 57.60% | 0.11% | T -> C |
mr1004 (All); LR P-value: 7.29E-07;
mr1005 (All); LR P-value: 7.63E-12; mr1059 (All); LR P-value: 2.12E-14; mr1146 (All); LR P-value: 8.42E-15; mr1150 (All); LR P-value: 1.43E-22; mr1441 (All); LR P-value: 5.12E-13; mr1675 (All); LR P-value: 1.08E-14; mr1874 (All); LR P-value: 9.84E-15; mr1950 (All); LR P-value: 3.22E-15; mr1158_2 (Ind_All); LR P-value: 2.38E-09; mr1195_2 (All); LR P-value: 6.60E-19; mr1383_2 (Ind_All); LR P-value: 1.57E-10; mr1520_2 (All); LR P-value: 1.37E-11; mr1654_2 (All); LR P-value: 8.20E-08; mr1874_2 (All); LR P-value: 1.14E-19 |
LOC_Os07g05190.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g05190.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 45.744; most accessible tissue: Callus, score: 77.773 |
| vg0702317034 (J) | chr07 | 2317034 | A | C | 99.40% | 0.00% | A -> C | NA |
LOC_Os07g05190.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 42.118; most accessible tissue: Callus, score: 87.473 |
| vg0702318162 (J) | chr07 | 2318162 | A | G | 56.70% | 0.25% | G -> A |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g05190.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 60.493; most accessible tissue: Zhenshan97 panicle, score: 83.904 |
|
| vg0702318558 (J) | chr07 | 2318558 | C | T | 57.40% | 0.00% | T -> C |
mr1005 (All); LR P-value: 3.77E-10;
mr1150 (All); LR P-value: 2.01E-21; mr1441 (All); LR P-value: 9.75E-13; mr1874 (All); LR P-value: 9.70E-14; mr1902 (All); LR P-value: 2.63E-11; mr1950 (All); LR P-value: 5.20E-15; mr1158_2 (Ind_All); LR P-value: 5.73E-10; mr1383_2 (Ind_All); LR P-value: 2.29E-10; mr1520_2 (All); LR P-value: 7.85E-12; mr1645_2 (All); LR P-value: 5.24E-08; mr1654_2 (All); LR P-value: 1.80E-07; mr1874_2 (All); LR P-value: 2.65E-18 |
LOC_Os07g05190.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 60.953; most accessible tissue: Zhenshan97 panicle, score: 91.030 |
| vg0702318694 (J) | chr07 | 2318694 | G | C | 57.50% | 0.04% | C -> G |
mr1004 (All); LR P-value: 7.43E-06;
mr1005 (All); LR P-value: 2.70E-10; mr1146 (All); LR P-value: 2.09E-14; mr1150 (All); LR P-value: 8.38E-22; mr1441 (All); LR P-value: 6.96E-13; mr1874 (All); LR P-value: 3.62E-14; mr1902 (All); LR P-value: 1.09E-11; mr1950 (All); LR P-value: 8.81E-15; mr1158_2 (Ind_All); LR P-value: 7.12E-10; mr1195_2 (All); LR P-value: 1.28E-18; mr1383_2 (Ind_All); LR P-value: 2.72E-10; mr1520_2 (All); LR P-value: 1.49E-11; mr1645_2 (All); LR P-value: 3.44E-08; mr1654_2 (All); LR P-value: 1.64E-07; mr1874_2 (All); LR P-value: 1.21E-18 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g05190.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 67.159; most accessible tissue: Zhenshan97 panicle, score: 91.536 |
| vg0702318720 (J) | chr07 | 2318720 | C | T | 57.70% | 0.00% | T -> C |
mr1004 (All); LR P-value: 5.87E-06;
mr1005 (All); LR P-value: 1.83E-10; mr1150 (All); LR P-value: 4.80E-22; mr1441 (All); LR P-value: 1.05E-12; mr1874 (All); LR P-value: 8.55E-14; mr1950 (All); LR P-value: 4.12E-15; mr1158_2 (Ind_All); LR P-value: 5.20E-10; mr1383_2 (Ind_All); LR P-value: 1.87E-10; mr1520_2 (All); LR P-value: 1.25E-11; mr1645_2 (All); LR P-value: 3.80E-08; mr1654_2 (All); LR P-value: 3.29E-07; mr1874_2 (All); LR P-value: 7.41E-19 |
LOC_Os07g05190.1 Alt: C| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 69.998; most accessible tissue: Zhenshan97 panicle, score: 92.403 |
| vg0702318727 (J) | chr07 | 2318727 | C | A | 99.40% | 0.00% | C -> A | NA |
LOC_Os07g05190.1 Alt: A| splice_region_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os07g05190.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 70.799; most accessible tissue: Zhenshan97 panicle, score: 92.784 |
| vg0702318929 (J) | chr07 | 2318929 | G | GAGA | 50.90% | 0.00% | GAGA -> G | NA |
LOC_Os07g05190.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 83.716; most accessible tissue: Callus, score: 97.610 |
| vg0702318932 (J) | chr07 | 2318932 | A | G | 99.80% | 0.00% | A -> G | NA |
LOC_Os07g05190.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)
The average chromatin accessibility score: 83.642; most accessible tissue: Callus, score: 97.610 |
| vg0702318944 (J) | chr07 | 2318944 | A | T | 99.40% | 0.00% | A -> T | NA |
LOC_Os07g05190.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 84.229; most accessible tissue: Callus, score: 97.610 |