11 variations found. LOC_Os11g19530 (expressed protein), ranging from 11,258,214 bp to 11,258,451 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1111258215 (J) | chr11 | 11258215 | C | T | 55.90% | 10.07% | T -> C |
mr1128 (All); LR P-value: 5.10E-10;
mr1302 (All); LR P-value: 1.57E-09; mr1315 (All); LR P-value: 7.99E-07; mr1336 (All); LR P-value: 3.63E-09; mr1376 (All); LR P-value: 7.87E-14; mr1383 (All); LR P-value: 2.32E-24; mr1392 (All); LR P-value: 3.08E-07; mr1431 (All); LR P-value: 7.87E-14; mr1488 (All); LR P-value: 4.01E-08; mr1521 (All); LR P-value: 2.02E-12; mr1604 (All); LR P-value: 1.20E-07; mr1636 (All); LR P-value: 5.66E-13; mr1641 (All); LR P-value: 1.85E-13; mr1647 (All); LR P-value: 6.49E-32; mr1683 (All); LR P-value: 2.54E-11; mr1723 (All); LR P-value: 3.45E-28; mr1767 (All); LR P-value: 6.18E-18; mr1776 (All); LR P-value: 2.66E-08; mr1779 (All); LR P-value: 3.28E-07; mr1810 (All); LR P-value: 2.28E-07; mr1838 (All); LR P-value: 3.20E-20; mr1839 (All); LR P-value: 2.14E-24; mr1886 (All); LR P-value: 1.63E-06; mr1909 (All); LR P-value: 1.23E-14 |
LOC_Os11g19530.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g19530.1 Alt: C| stop_lost&splice_region_variant HIGH(snpEff)/stop_lost(CooVar) The average chromatin accessibility score: 70.724; most accessible tissue: Zhenshan97 panicle, score: 86.432 |
| vg1111258237 (J) | chr11 | 11258237 | A | G | 90.30% | 8.97% | A -> G | NA |
LOC_Os11g19530.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g19530.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 72.686; most accessible tissue: Zhenshan97 panicle, score: 88.062 |
| vg1111258252 (J) | chr11 | 11258252 | G | T | 56.00% | 10.03% | T -> G |
mr1302 (All); LR P-value: 9.32E-10;
mr1315 (All); LR P-value: 5.69E-07; mr1336 (All); LR P-value: 1.88E-09; mr1376 (All); LR P-value: 4.75E-14; mr1383 (All); LR P-value: 3.91E-24; mr1386 (All); LR P-value: 5.60E-12; mr1392 (All); LR P-value: 1.77E-07; mr1431 (All); LR P-value: 4.75E-14; mr1488 (All); LR P-value: 2.41E-08; mr1521 (All); LR P-value: 2.37E-12; mr1604 (All); LR P-value: 8.51E-08; mr1636 (All); LR P-value: 5.28E-13; mr1641 (All); LR P-value: 2.22E-13; mr1647 (All); LR P-value: 1.52E-31; mr1683 (All); LR P-value: 1.99E-11; mr1701 (All); LR P-value: 3.04E-13; mr1723 (All); LR P-value: 6.75E-28; mr1767 (All); LR P-value: 4.26E-18; mr1776 (All); LR P-value: 5.54E-09; mr1779 (All); LR P-value: 1.69E-07; mr1810 (All); LR P-value: 1.50E-07; mr1838 (All); LR P-value: 4.33E-20; mr1839 (All); LR P-value: 1.89E-24; mr1886 (All); LR P-value: 1.15E-06; mr1909 (All); LR P-value: 1.02E-14 |
LOC_Os11g19530.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g19530.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 73.736; most accessible tissue: Zhenshan97 panicle, score: 88.350 |
| vg1111258291 (J) | chr11 | 11258291 | T | C | 61.50% | 10.43% | T -> C | NA |
LOC_Os11g19530.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g19530.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 73.375; most accessible tissue: Zhenshan97 panicle, score: 88.625 |
| vg1111258296 (J) | chr11 | 11258296 | CTG | C | 90.20% | 9.52% | CTG -> C | NA |
LOC_Os11g19530.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g19530.1 Alt: C/frameshift_variant(CooVar) The average chromatin accessibility score: 73.147; most accessible tissue: Zhenshan97 panicle, score: 88.625 |
| vg1111258312 (J) | chr11 | 11258312 | T | C | 55.40% | 10.30% | C -> T |
Yield (All); LR P-value: 3.82E-19;
mr1302 (All); LR P-value: 1.42E-09; mr1361 (All); LR P-value: 2.55E-14; mr1376 (All); LR P-value: 4.86E-14; mr1383 (All); LR P-value: 1.64E-23; mr1392 (All); LR P-value: 9.75E-07; mr1431 (All); LR P-value: 4.86E-14; mr1604 (All); LR P-value: 1.82E-07; mr1636 (All); LR P-value: 2.38E-13; mr1641 (All); LR P-value: 1.04E-12; mr1683 (All); LR P-value: 3.90E-11; mr1723 (All); LR P-value: 2.72E-27; mr1758 (All); LR P-value: 6.29E-86; mr1776 (All); LR P-value: 9.75E-09; mr1779 (All); LR P-value: 1.22E-07; mr1810 (All); LR P-value: 2.85E-07; mr1839 (All); LR P-value: 4.03E-24; mr1886 (All); LR P-value: 1.42E-06 |
LOC_Os11g19530.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os11g19530.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 74.565; most accessible tissue: Zhenshan97 panicle, score: 89.389 |
| vg1111258328 (J) | chr11 | 11258328 | G | A | 89.70% | 9.59% | G -> A | NA |
LOC_Os11g19530.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g19530.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 73.877; most accessible tissue: Zhenshan97 panicle, score: 91.030 |
| vg1111258336 (J) | chr11 | 11258336 | C | T | 66.10% | 9.94% | C -> T |
mr1277 (Ind_All); LR P-value: 1.57E-07;
mr1609 (Ind_All); LR P-value: 6.32E-06; mr1806 (All); LR P-value: 2.27E-08; mr1829 (Ind_All); LR P-value: 3.46E-09; mr1902 (Ind_All); LR P-value: 1.12E-07; mr1154_2 (Ind_All); LR P-value: 1.74E-06; mr1829_2 (Ind_All); LR P-value: 1.79E-10; mr1842_2 (Ind_All); LR P-value: 8.96E-07; mr1892_2 (All); LR P-value: 6.36E-06; mr1902_2 (Ind_All); LR P-value: 1.43E-09 |
LOC_Os11g19530.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os11g19530.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 73.423; most accessible tissue: Zhenshan97 panicle, score: 91.206 |
| vg1111258351 (J) | chr11 | 11258351 | G | A | 90.30% | 9.23% | G -> A | NA |
LOC_Os11g19530.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g19530.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 75.451; most accessible tissue: Zhenshan97 panicle, score: 91.992 |
| vg1111258385 (J) | chr11 | 11258385 | G | T | 88.30% | 9.39% | G -> T | NA |
LOC_Os11g19530.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g19530.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 76.464; most accessible tissue: Zhenshan97 panicle, score: 92.133 |
| vg1111258406 (J) | chr11 | 11258406 | C | A | 66.10% | 10.16% | C -> A |
mr1077 (Ind_All); LR P-value: 2.12E-06;
mr1277 (Ind_All); LR P-value: 4.31E-07; mr1806 (All); LR P-value: 7.87E-09; mr1829 (Ind_All); LR P-value: 1.47E-10; mr1842 (Ind_All); LR P-value: 1.96E-06; mr1892 (All); LR P-value: 6.24E-06; mr1902 (Ind_All); LR P-value: 6.94E-09; mr1154_2 (Ind_All); LR P-value: 5.85E-07; mr1441_2 (Ind_All); LR P-value: 1.39E-07; mr1829_2 (Ind_All); LR P-value: 6.68E-11; mr1842_2 (Ind_All); LR P-value: 1.16E-06; mr1892_2 (All); LR P-value: 2.88E-06; mr1902_2 (Ind_All); LR P-value: 3.36E-09; mr1933_2 (Ind_All); LR P-value: 6.72E-07 |
LOC_Os11g19530.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g19530.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 76.994; most accessible tissue: Zhenshan97 panicle, score: 92.533 |