7 variations found. LOC_Os07g05180 (Skp1 family; dimerisation domain containing protein; expressed), ranging from 2,311,417 bp to 2,311,912 bp (including 0 kb upstream and 0 kb downstream of the gene).
| 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0702311463 (J) | chr07 | 2311463 | A | G | 58.00% | 0.00% | G -> A |
mr1004 (All); LR P-value: 1.94E-07;
mr1005 (All); LR P-value: 6.86E-13; mr1005 (Ind_All); LR P-value: 5.04E-06; mr1146 (All); LR P-value: 7.82E-15; mr1150 (All); LR P-value: 3.30E-22; mr1874 (All); LR P-value: 1.14E-13; mr1950 (All); LR P-value: 2.97E-15; mr1158_2 (Ind_All); LR P-value: 1.02E-09; mr1195_2 (All); LR P-value: 8.49E-19; mr1383_2 (Ind_All); LR P-value: 2.31E-11; mr1654_2 (All); LR P-value: 1.55E-07; mr1874_2 (All); LR P-value: 2.51E-19 |
LOC_Os07g05180.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 62.697; most accessible tissue: Zhenshan97 panicle, score: 83.410 |
| vg0702311601 (J) | chr07 | 2311601 | G | T | 99.30% | 0.00% | G -> T | NA |
LOC_Os07g05180.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 60.410; most accessible tissue: Zhenshan97 panicle, score: 82.888 |
| vg0702311679 (J) | chr07 | 2311679 | A | G | 93.70% | 0.00% | A -> G |
mr1006 (All); LR P-value: 3.71E-06;
mr1030 (All); LR P-value: 3.81E-06; mr1052 (All); LR P-value: 6.47E-06; mr1073 (All); LR P-value: 4.50E-07; mr1095 (All); LR P-value: 1.76E-25; mr1098 (All); LR P-value: 4.20E-37; mr1099 (All); LR P-value: 3.76E-33; mr1101 (All); LR P-value: 6.45E-31; mr1113 (All); LR P-value: 5.97E-16; mr1114 (All); LR P-value: 1.33E-18; mr1117 (All); LR P-value: 4.90E-21; mr1119 (All); LR P-value: 1.55E-16; mr1120 (All); LR P-value: 1.26E-23; mr1123 (All); LR P-value: 2.35E-28; mr1146 (All); LR P-value: 2.39E-14; mr1158 (All); LR P-value: 2.35E-15; mr1168 (All); LR P-value: 2.81E-21; mr1210 (All); LR P-value: 3.13E-21; mr1230 (All); LR P-value: 4.40E-07; mr1240 (All); LR P-value: 6.82E-19; mr1247 (All); LR P-value: 1.24E-23; mr1262 (All); LR P-value: 4.37E-06; mr1305 (All); LR P-value: 1.30E-23; mr1345 (All); LR P-value: 1.36E-06; mr1365 (All); LR P-value: 2.32E-08; mr1367 (All); LR P-value: 6.18E-06; mr1382 (All); LR P-value: 1.89E-06; mr1427 (All); LR P-value: 2.62E-06; mr1442 (All); LR P-value: 1.60E-08; mr1496 (All); LR P-value: 7.25E-15; mr1499 (All); LR P-value: 4.40E-12; mr1515 (All); LR P-value: 7.63E-19; mr1523 (All); LR P-value: 4.70E-06; mr1549 (All); LR P-value: 1.04E-37; mr1550 (All); LR P-value: 3.66E-45; mr1586 (All); LR P-value: 6.62E-27; mr1589 (All); LR P-value: 1.91E-26; mr1612 (All); LR P-value: 1.54E-11; mr1621 (All); LR P-value: 5.68E-07; mr1634 (All); LR P-value: 1.69E-07; mr1649 (All); LR P-value: 4.31E-13; mr1665 (All); LR P-value: 2.91E-06; mr1696 (All); LR P-value: 1.97E-11; mr1727 (All); LR P-value: 7.08E-06; mr1757 (All); LR P-value: 3.72E-38; mr1765 (All); LR P-value: 3.75E-17; mr1858 (All); LR P-value: 2.90E-28; mr1859 (All); LR P-value: 2.64E-28; mr1868 (All); LR P-value: 4.74E-28; mr1911 (All); LR P-value: 1.92E-17; mr1918 (All); LR P-value: 1.01E-12; mr1931 (All); LR P-value: 1.24E-06; mr1936 (All); LR P-value: 4.73E-18; mr1961 (All); LR P-value: 1.93E-22; mr1047_2 (All); LR P-value: 1.39E-11; mr1095_2 (All); LR P-value: 1.14E-21; mr1098_2 (All); LR P-value: 1.59E-34; mr1099_2 (All); LR P-value: 7.71E-27; mr1117_2 (All); LR P-value: 4.71E-18; mr1120_2 (All); LR P-value: 2.37E-21; mr1123_2 (All); LR P-value: 7.68E-22; mr1240_2 (All); LR P-value: 9.41E-18; mr1305_2 (All); LR P-value: 2.57E-20; mr1409_2 (All); LR P-value: 7.13E-12; mr1510_2 (All); LR P-value: 6.45E-08; mr1549_2 (All); LR P-value: 1.02E-31; mr1550_2 (All); LR P-value: 2.09E-43; mr1792_2 (All); LR P-value: 1.19E-06; mr1803_2 (All); LR P-value: 1.21E-13; mr1815_2 (All); LR P-value: 7.18E-07; mr1911_2 (All); LR P-value: 1.66E-15; mr1936_2 (All); LR P-value: 1.44E-14 |
LOC_Os07g05180.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 62.842; most accessible tissue: Zhenshan97 panicle, score: 78.302 |
| vg0702311691 (J) | chr07 | 2311691 | A | G | 50.70% | 0.36% | G -> A |
LOC_Os07g05180.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g05180.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 61.645; most accessible tissue: Zhenshan97 panicle, score: 78.302 |
|
| vg0702311705 (J) | chr07 | 2311705 | C | T | 57.80% | 0.32% | T -> C |
mr1004 (All); LR P-value: 1.76E-06;
mr1005 (All); LR P-value: 1.53E-11; mr1146 (All); LR P-value: 4.82E-15; mr1150 (All); LR P-value: 8.04E-22; mr1874 (All); LR P-value: 2.39E-14; mr1950 (All); LR P-value: 8.37E-15; mr1158_2 (Ind_All); LR P-value: 1.92E-10; mr1195_2 (All); LR P-value: 1.38E-18; mr1383_2 (Ind_All); LR P-value: 1.26E-11; mr1520_2 (All); LR P-value: 9.18E-12; mr1645_2 (All); LR P-value: 7.40E-08; mr1654_2 (All); LR P-value: 2.23E-07; mr1874_2 (All); LR P-value: 4.81E-19 |
LOC_Os07g05180.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g05180.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 65.020; most accessible tissue: Zhenshan97 panicle, score: 80.486 |
| vg0702311882 (J) | chr07 | 2311882 | C | T | 94.70% | 0.00% | C -> T | NA |
LOC_Os07g05180.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 63.501; most accessible tissue: Zhenshan97 panicle, score: 77.482 |
| STR0702311456 (J) | chr07 | 2311456 | CGGCAGC G | CGGCAGC A | 50.00% | 0.00% | CGGCAGCG -> CGGCAGCA | NA |
|