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Search Results:

10 variations found. LOC_Os02g43250 (receptor-like protein kinase precursor; putative; expressed), ranging from 26,052,819 bp to 26,054,216 bp (including 0 kb upstream and 0 kb downstream of the gene).

Variation Map (with Chromatin Accessibility Map/ Non-coding Varation Scores Map) in Searched Region:

The 'big effect' variations are marked out:

ColorExplainDetails
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.

Detailed Variation Information:

Var ID Chrom Position Primary Allele Secondary Allele Primary Allele Frequency DEL Frequency Var GWAS Results Effect
vg0226052907 (J) chr02 26052907 T G 69.70% 0.00% G -> T
mr1239 (All); LR P-value: 4.06E-13;
mr1853 (All); LR P-value: 5.97E-13;
mr1133_2 (All); LR P-value: 6.73E-15;
mr1667_2 (All); LR P-value: 5.47E-11
LOC_Os02g43250.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 98.483; most accessible tissue: Zhenshan97 panicle, score: 99.663
vg0226052991 (J) chr02 26052991 C T 79.70% 0.00% C -> T
mr1069 (Ind_All); LR P-value: 1.79E-07;
mr1072 (Ind_All); LR P-value: 7.14E-08;
mr1074 (Ind_All); LR P-value: 1.22E-08;
mr1075 (Ind_All); LR P-value: 3.18E-07;
mr1077 (Ind_All); LR P-value: 1.59E-07;
mr1080 (Ind_All); LR P-value: 9.09E-06;
mr1124 (Ind_All); LR P-value: 1.28E-07;
mr1130 (Ind_All); LR P-value: 6.67E-08;
mr1148 (Ind_All); LR P-value: 5.09E-06;
mr1150 (Ind_All); LR P-value: 4.76E-06;
mr1180 (Ind_All); LR P-value: 1.10E-07;
mr1193 (All); LR P-value: 7.64E-08;
mr1202 (Ind_All); LR P-value: 7.45E-07;
mr1441 (Ind_All); LR P-value: 6.49E-07;
mr1861 (Ind_All); LR P-value: 1.28E-07;
mr1918 (Ind_All); LR P-value: 1.52E-09;
mr1934 (Ind_All); LR P-value: 1.49E-08;
mr1935 (Ind_All); LR P-value: 3.73E-09;
mr1962 (Ind_All); LR P-value: 1.39E-08;
mr1072_2 (Ind_All); LR P-value: 1.22E-10;
mr1074_2 (Ind_All); LR P-value: 3.24E-06;
mr1075_2 (Ind_All); LR P-value: 2.16E-11;
mr1077_2 (Ind_All); LR P-value: 1.49E-12;
mr1098_2 (Ind_All); LR P-value: 5.80E-06;
mr1124_2 (Ind_All); LR P-value: 1.92E-11;
mr1149_2 (Ind_All); LR P-value: 7.05E-11;
mr1150_2 (Ind_All); LR P-value: 2.52E-08;
mr1174_2 (Ind_All); LR P-value: 2.32E-08;
mr1222_2 (Ind_All); LR P-value: 1.35E-07;
mr1332_2 (Ind_All); LR P-value: 2.41E-06;
mr1347_2 (Ind_All); LR P-value: 5.00E-10;
mr1441_2 (Ind_All); LR P-value: 4.16E-12;
mr1558_2 (Ind_All); LR P-value: 5.47E-06;
mr1592_2 (Ind_All); LR P-value: 1.40E-06;
mr1598_2 (Ind_All); LR P-value: 3.11E-10;
mr1619_2 (Ind_All); LR P-value: 5.44E-07;
mr1861_2 (Ind_All); LR P-value: 2.63E-15;
mr1895_2 (Ind_All); LR P-value: 2.77E-06;
mr1918_2 (Ind_All); LR P-value: 1.73E-06;
mr1928_2 (Ind_All); LR P-value: 1.24E-06;
mr1931_2 (Ind_All); LR P-value: 5.14E-06;
mr1962_2 (Ind_All); LR P-value: 5.06E-13
LOC_Os02g43250.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 98.902; most accessible tissue: Zhenshan97 panicle, score: 99.739
vg0226053265 (J) chr02 26053265 C T 98.50% 0.00% C -> T NA
LOC_Os02g43250.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 97.276; most accessible tissue: Zhenshan97 panicle, score: 99.379
vg0226053379 (J) chr02 26053379 C A 93.40% 0.80% C -> A NA
LOC_Os02g43250.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g43250.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 92.713; most accessible tissue: Zhenshan97 panicle, score: 98.901
vg0226053588 (J) chr02 26053588 C T 79.50% 0.00% C -> T
mr1069 (Ind_All); LR P-value: 3.30E-07;
mr1072 (Ind_All); LR P-value: 1.25E-07;
mr1074 (Ind_All); LR P-value: 3.41E-08;
mr1075 (Ind_All); LR P-value: 4.79E-07;
mr1077 (Ind_All); LR P-value: 5.33E-07;
mr1124 (Ind_All); LR P-value: 1.89E-07;
mr1130 (Ind_All); LR P-value: 1.44E-07;
mr1180 (Ind_All); LR P-value: 1.62E-07;
mr1193 (All); LR P-value: 5.35E-08;
mr1202 (Ind_All); LR P-value: 1.05E-06;
mr1441 (Ind_All); LR P-value: 1.40E-06;
mr1861 (Ind_All); LR P-value: 2.61E-07;
mr1918 (Ind_All); LR P-value: 2.99E-09;
mr1934 (Ind_All); LR P-value: 6.07E-09;
mr1935 (Ind_All); LR P-value: 1.27E-08;
mr1962 (Ind_All); LR P-value: 5.39E-08;
mr1072_2 (Ind_All); LR P-value: 2.37E-10;
mr1074_2 (Ind_All); LR P-value: 3.55E-06;
mr1075_2 (Ind_All); LR P-value: 5.49E-11;
mr1077_2 (Ind_All); LR P-value: 1.55E-11;
mr1098_2 (Ind_All); LR P-value: 6.99E-06;
mr1124_2 (Ind_All); LR P-value: 3.56E-11;
mr1149_2 (Ind_All); LR P-value: 1.74E-10;
mr1150_2 (Ind_All); LR P-value: 4.92E-08;
mr1174_2 (Ind_All); LR P-value: 9.55E-08;
mr1222_2 (Ind_All); LR P-value: 1.51E-07;
mr1332_2 (Ind_All); LR P-value: 7.56E-06;
mr1347_2 (Ind_All); LR P-value: 1.13E-09;
mr1441_2 (Ind_All); LR P-value: 1.30E-11;
mr1558_2 (Ind_All); LR P-value: 8.71E-06;
mr1592_2 (Ind_All); LR P-value: 3.66E-06;
mr1598_2 (Ind_All); LR P-value: 1.28E-09;
mr1619_2 (Ind_All); LR P-value: 6.84E-07;
mr1861_2 (Ind_All); LR P-value: 1.32E-14;
mr1918_2 (Ind_All); LR P-value: 3.19E-06;
mr1928_2 (Ind_All); LR P-value: 1.29E-06;
mr1931_2 (Ind_All); LR P-value: 8.80E-06;
mr1934_2 (Ind_All); LR P-value: 3.85E-08;
mr1962_2 (Ind_All); LR P-value: 1.47E-12
LOC_Os02g43250.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 91.592; most accessible tissue: Zhenshan97 panicle, score: 97.974
vg0226054006 (J) chr02 26054006 C T 93.40% 0.00% C -> T NA
LOC_Os02g43250.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 96.188; most accessible tissue: Zhenshan97 panicle, score: 99.382
vg0226054012 (J) chr02 26054012 C A 95.70% 0.00% C -> A NA
LOC_Os02g43250.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 96.342; most accessible tissue: Zhenshan97 panicle, score: 99.416
vg0226054119 (J) chr02 26054119 CGGA C 98.50% 0.00% CGGA -> C NA
LOC_Os02g43250.1 Alt: C| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 97.088; most accessible tissue: Zhenshan97 panicle, score: 99.569
vg0226054186 (J) chr02 26054186 A G 63.90% 0.00% G -> A NA
LOC_Os02g43250.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g43260.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 97.455; most accessible tissue: Callus, score: 99.794
STR0226054185 (J) chr02 26054185 GA GG 59.00% 0.00% GG -> GA NA