9 variations found. LOC_Os10g38800 (leucine-rich repeat transmembrane protein kinase; putative; expressed), ranging from 20,652,204 bp to 20,654,875 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1020652229 (J) | chr10 | 20652229 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os10g38800.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g38790.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 60.481; most accessible tissue: Callus, score: 90.967 |
| vg1020652779 (J) | chr10 | 20652779 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os10g38800.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os10g38790.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 71.850; most accessible tissue: Zhenshan97 young leaf, score: 90.728 |
| vg1020652875 (J) | chr10 | 20652875 | A | G | 62.70% | 0.00% | G -> A |
mr1509 (All); LMM P-value: 6.71E-08; LR P-value: 2.39E-51;
mr1509 (Jap_All); LR P-value: 5.61E-06; mr1558 (All); LMM P-value: 6.40E-10; LR P-value: 6.65E-59; mr1558 (Jap_All); LR P-value: 1.58E-06; mr1990 (All); LR P-value: 1.37E-06; mr1509_2 (All); LMM P-value: 5.14E-12; LR P-value: 3.45E-62; mr1509_2 (Jap_All); LMM P-value: 9.38E-06; LR P-value: 4.72E-09; mr1514_2 (All); LR P-value: 1.43E-13; mr1558_2 (All); LMM P-value: 2.22E-16; LR P-value: 1.92E-81; mr1558_2 (Jap_All); LMM P-value: 3.86E-07; LR P-value: 4.35E-13 |
LOC_Os10g38800.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 67.445; most accessible tissue: Zhenshan97 flag leaf, score: 87.755 |
| vg1020652975 (J) | chr10 | 20652975 | C | A | 99.70% | 0.00% | C -> A | NA |
LOC_Os10g38800.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 69.082; most accessible tissue: Zhenshan97 flag leaf, score: 87.755 |
| vg1020653028 (J) | chr10 | 20653028 | G | A | 66.80% | 0.00% | A -> G |
mr1509 (All); LR P-value: 3.94E-48;
mr1509 (Jap_All); LR P-value: 1.97E-06; mr1558 (All); LMM P-value: 5.13E-08; LR P-value: 3.85E-61; mr1558 (Jap_All); LR P-value: 8.36E-07; mr1746 (All); LR P-value: 7.80E-11; mr1862 (All); LR P-value: 7.18E-24; mr1133_2 (All); LR P-value: 1.06E-14; mr1399_2 (All); LR P-value: 1.64E-08; mr1509_2 (All); LMM P-value: 1.28E-07; LR P-value: 1.79E-55; mr1509_2 (Jap_All); LR P-value: 6.77E-10; mr1558_2 (All); LMM P-value: 3.64E-12; LR P-value: 1.11E-84; mr1558_2 (Jap_All); LR P-value: 2.12E-12; mr1662_2 (All); LR P-value: 1.58E-06; mr1667_2 (All); LR P-value: 1.08E-11; mr1731_2 (All); LR P-value: 5.33E-20; mr1746_2 (All); LR P-value: 3.73E-20; mr1805_2 (Jap_All); LR P-value: 3.59E-09; mr1940_2 (All); LR P-value: 2.85E-08; mr1950_2 (All); LR P-value: 1.23E-14 |
LOC_Os10g38800.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 70.087; most accessible tissue: Zhenshan97 flag leaf, score: 89.283 |
| vg1020653920 (J) | chr10 | 20653920 | G | C | 99.90% | 0.00% | G -> C | NA |
LOC_Os10g38800.1 Alt: C| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 57.639; most accessible tissue: Zhenshan97 young leaf, score: 80.325 |
| vg1020653962 (J) | chr10 | 20653962 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os10g38800.1 Alt: A| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 59.955; most accessible tissue: Zhenshan97 panicle, score: 81.135 |
| vg1020654113 (J) | chr10 | 20654113 | ACAG | A | 99.80% | 0.00% | ACAG -> A | NA |
LOC_Os10g38800.1 Alt: A| inframe_deletion MODERATE(snpEff)
The average chromatin accessibility score: 58.742; most accessible tissue: Zhenshan97 panicle, score: 84.374 |
| vg1020654458 (J) | chr10 | 20654458 | T | C | 62.70% | 0.00% | C -> T |
mr1509 (All); LMM P-value: 2.26E-08; LR P-value: 3.06E-52;
mr1509 (Jap_All); LR P-value: 5.61E-06; mr1558 (All); LMM P-value: 9.21E-10; LR P-value: 2.90E-59; mr1558 (Jap_All); LR P-value: 1.58E-06; mr1862 (All); LR P-value: 2.95E-23; mr1990 (All); LR P-value: 2.73E-06; mr1509_2 (All); LMM P-value: 8.00E-14; LR P-value: 1.81E-64; mr1509_2 (Jap_All); LMM P-value: 9.38E-06; LR P-value: 4.72E-09; mr1514_2 (All); LR P-value: 2.05E-13; mr1558_2 (All); LMM P-value: 5.96E-17; LR P-value: 1.26E-82; mr1558_2 (Jap_All); LMM P-value: 3.86E-07; LR P-value: 4.35E-13 |
LOC_Os10g38800.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 67.965; most accessible tissue: Zhenshan97 flower, score: 87.611 |