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Search Results:

19 variations found. LOC_Os06g20010 (RNA recognition motif containing protein; putative; expressed), ranging from 11,474,472 bp to 11,474,742 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
vg0611474485 (J) chr06 11474485 G A 98.40% 0.00% G -> A NA
LOC_Os06g20010.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 71.859; most accessible tissue: Zhenshan97 young leaf, score: 88.759
vg0611474489 (J) chr06 11474489 C T 98.90% 0.00% C -> T NA
LOC_Os06g20010.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 71.007; most accessible tissue: Zhenshan97 young leaf, score: 88.127
vg0611474511 (J) chr06 11474511 C T 99.40% 0.00% C -> T NA
LOC_Os06g20010.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os06g20000.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os06g20020.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 71.275; most accessible tissue: Zhenshan97 young leaf, score: 87.584
vg0611474516 (J) chr06 11474516 C T 52.00% 0.04% C -> T
mr1037 (All); LR P-value: 1.66E-27;
mr1065 (All); LMM P-value: 1.00E-07; LR P-value: 1.67E-69;
mr1065 (Ind_All); LR P-value: 8.49E-12;
mr1067 (All); LR P-value: 1.77E-47;
mr1068 (All); LMM P-value: 5.40E-08; LR P-value: 1.42E-68;
mr1068 (Ind_All); LMM P-value: 8.49E-06; LR P-value: 1.39E-11;
mr1078 (All); LMM P-value: 6.36E-06; LR P-value: 2.37E-59;
mr1078 (Ind_All); LR P-value: 1.01E-07;
mr1087 (All); LMM P-value: 1.04E-07; LR P-value: 2.47E-64;
mr1087 (Ind_All); LR P-value: 5.31E-10;
mr1090 (All); LMM P-value: 1.73E-06; LR P-value: 2.77E-60;
mr1090 (Ind_All); LR P-value: 4.58E-07;
mr1091 (All); LMM P-value: 9.49E-07; LR P-value: 3.84E-49;
mr1091 (Ind_All); LR P-value: 9.26E-10;
mr1094 (All); LMM P-value: 4.63E-06; LR P-value: 1.50E-45;
mr1096 (All); LMM P-value: 5.43E-06; LR P-value: 3.39E-60;
mr1096 (Ind_All); LR P-value: 1.48E-07;
mr1108 (All); LR P-value: 5.14E-55;
mr1108 (Ind_All); LR P-value: 1.00E-09;
mr1110 (All); LR P-value: 1.97E-44;
mr1111 (All); LR P-value: 2.23E-56;
mr1111 (Ind_All); LR P-value: 1.39E-08;
mr1112 (All); LR P-value: 9.27E-55;
mr1112 (Ind_All); LR P-value: 1.56E-08;
mr1121 (All); LMM P-value: 5.37E-07; LR P-value: 2.30E-59;
mr1121 (Ind_All); LR P-value: 5.24E-09;
mr1131 (All); LR P-value: 3.82E-20;
mr1144 (All); LMM P-value: 1.89E-07; LR P-value: 1.62E-57;
mr1144 (Ind_All); LMM P-value: 6.86E-06; LR P-value: 1.07E-10;
mr1200 (All); LR P-value: 8.86E-50;
mr1200 (Ind_All); LR P-value: 1.51E-07;
mr1211 (All); LR P-value: 7.44E-54;
mr1234 (All); LR P-value: 9.22E-52;
mr1237 (All); LR P-value: 3.02E-37;
mr1237 (Ind_All); LR P-value: 2.13E-07;
mr1270 (All); LR P-value: 5.40E-13;
mr1426 (All); LR P-value: 1.24E-28;
mr1526 (All); LR P-value: 4.33E-48;
mr1526 (Ind_All); LR P-value: 1.83E-07;
mr1877 (All); LR P-value: 6.55E-30;
mr1878 (All); LR P-value: 2.66E-32;
mr1065_2 (All); LMM P-value: 7.24E-06; LR P-value: 1.04E-77;
mr1065_2 (Ind_All); LMM P-value: 1.95E-06; LR P-value: 1.62E-14;
mr1067_2 (All); LR P-value: 5.34E-61;
mr1067_2 (Ind_All); LR P-value: 9.45E-11;
mr1068_2 (All); LMM P-value: 1.07E-07; LR P-value: 1.97E-82;
mr1068_2 (Ind_All); LMM P-value: 8.72E-08; LR P-value: 1.63E-15;
mr1078_2 (All); LR P-value: 3.50E-72;
mr1078_2 (Ind_All); LR P-value: 2.24E-09;
mr1087_2 (All); LMM P-value: 4.58E-08; LR P-value: 1.12E-75;
mr1087_2 (Ind_All); LMM P-value: 1.10E-07; LR P-value: 2.33E-13;
mr1090_2 (All); LR P-value: 1.48E-66;
mr1090_2 (Ind_All); LMM P-value: 7.99E-07; LR P-value: 1.26E-08;
mr1091_2 (All); LMM P-value: 2.54E-06; LR P-value: 4.64E-61;
mr1091_2 (Ind_All); LR P-value: 1.31E-11;
mr1094_2 (All); LR P-value: 1.47E-54;
mr1094_2 (Ind_All); LR P-value: 4.25E-08;
mr1096_2 (All); LR P-value: 9.10E-70;
mr1096_2 (Ind_All); LR P-value: 3.08E-10;
mr1108_2 (All); LMM P-value: 1.43E-06; LR P-value: 2.56E-66;
mr1108_2 (Ind_All); LMM P-value: 1.77E-06; LR P-value: 2.06E-12;
mr1110_2 (All); LR P-value: 4.53E-48;
mr1110_2 (Ind_All); LR P-value: 4.35E-08;
mr1111_2 (All); LMM P-value: 2.26E-07; LR P-value: 1.55E-64;
mr1111_2 (Ind_All); LMM P-value: 3.47E-09; LR P-value: 6.04E-14;
mr1112_2 (All); LMM P-value: 1.40E-06; LR P-value: 1.02E-74;
mr1112_2 (Ind_All); LMM P-value: 6.27E-06; LR P-value: 7.45E-13;
mr1121_2 (All); LR P-value: 1.44E-59;
mr1121_2 (Ind_All); LR P-value: 5.68E-09;
mr1131_2 (All); LR P-value: 1.88E-18;
mr1144_2 (All); LMM P-value: 6.01E-06; LR P-value: 2.07E-63;
mr1144_2 (Ind_All); LMM P-value: 2.28E-06; LR P-value: 1.34E-11;
mr1199_2 (All); LR P-value: 1.77E-17;
mr1200_2 (All); LR P-value: 2.93E-61;
mr1200_2 (Ind_All); LR P-value: 4.14E-11;
mr1211_2 (All); LMM P-value: 1.34E-06; LR P-value: 5.49E-63;
mr1211_2 (Ind_All); LMM P-value: 8.91E-07; LR P-value: 2.07E-09;
mr1218_2 (All); LR P-value: 7.49E-19;
mr1221_2 (All); LR P-value: 2.84E-34;
mr1234_2 (All); LMM P-value: 6.28E-06; LR P-value: 1.80E-69;
mr1234_2 (Ind_All); LR P-value: 4.86E-12;
mr1244_2 (All); LR P-value: 2.14E-24;
mr1341_2 (All); LR P-value: 4.84E-06;
mr1526_2 (All); LMM P-value: 4.18E-06; LR P-value: 5.29E-64;
mr1526_2 (Ind_All); LMM P-value: 3.47E-07; LR P-value: 3.06E-13;
mr1686_2 (All); LR P-value: 4.72E-15;
mr1690_2 (All); LR P-value: 4.17E-08;
mr1877_2 (All); LR P-value: 6.85E-24
LOC_Os06g20010.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g20010.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 71.050; most accessible tissue: Zhenshan97 young leaf, score: 87.299
vg0611474533 (J) chr06 11474533 C A 95.50% 0.00% C -> A NA
LOC_Os06g20010.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 72.551; most accessible tissue: Zhenshan97 young leaf, score: 87.859
vg0611474543 (J) chr06 11474543 G A 99.50% 0.00% G -> A NA
LOC_Os06g20010.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os06g20000.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os06g20020.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 72.884; most accessible tissue: Zhenshan97 young leaf, score: 88.759
vg0611474546 (J) chr06 11474546 T C 99.50% 0.00% T -> C NA
LOC_Os06g20010.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os06g20000.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
LOC_Os06g20020.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 73.162; most accessible tissue: Zhenshan97 young leaf, score: 88.878
vg0611474584 (J) chr06 11474584 A G 99.60% 0.00% A -> G NA
LOC_Os06g20010.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os06g20000.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os06g20020.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 73.163; most accessible tissue: Zhenshan97 young leaf, score: 90.175
vg0611474586 (J) chr06 11474586 C T 98.40% 0.00% C -> T NA
LOC_Os06g20010.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 73.403; most accessible tissue: Zhenshan97 young leaf, score: 90.175
vg0611474617 (J) chr06 11474617 C T 99.80% 0.00% C -> T NA
LOC_Os06g20010.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os06g20000.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os06g20020.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 73.688; most accessible tissue: Zhenshan97 young leaf, score: 90.175
vg0611474634 (J) chr06 11474634 G A 95.50% 0.00% G -> A NA
LOC_Os06g20010.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 74.079; most accessible tissue: Zhenshan97 young leaf, score: 90.638
vg0611474656 (J) chr06 11474656 G A 95.00% 0.00% G -> A NA
LOC_Os06g20010.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 73.711; most accessible tissue: Zhenshan97 young leaf, score: 90.815
vg0611474663 (J) chr06 11474663 C T 64.50% 0.00% T -> C
mr1020 (All); LR P-value: 6.10E-22;
mr1087 (All); LR P-value: 1.75E-60;
mr1090 (All); LR P-value: 3.79E-56;
mr1138 (All); LR P-value: 4.80E-12;
mr1139 (All); LR P-value: 6.60E-39;
mr1144 (Jap_All); LMM P-value: 8.63E-06; LR P-value: 8.62E-06;
mr1147 (All); LR P-value: 5.94E-16;
mr1165 (Jap_All); LMM P-value: 3.37E-06; LR P-value: 3.37E-06;
mr1181 (All); LR P-value: 1.93E-26;
mr1211 (All); LR P-value: 1.79E-52;
mr1299 (All); LR P-value: 2.13E-09;
mr1478 (Jap_All); LMM P-value: 5.57E-08; LR P-value: 5.57E-08;
mr1763 (All); LR P-value: 1.08E-07;
mr1807 (All); LR P-value: 4.55E-15;
mr1938 (All); LR P-value: 9.36E-12;
mr1971 (All); LR P-value: 2.26E-21;
mr1971 (Jap_All); LMM P-value: 3.21E-06;
mr1068_2 (All); LR P-value: 1.38E-62;
mr1090_2 (All); LR P-value: 7.12E-61;
mr1165_2 (All); LR P-value: 9.07E-19;
mr1165_2 (Jap_All); LMM P-value: 4.93E-06;
mr1211_2 (All); LR P-value: 1.34E-55;
mr1477_2 (All); LR P-value: 9.87E-31;
mr1477_2 (Jap_All); LMM P-value: 2.95E-06; LR P-value: 2.95E-06;
mr1578_2 (All); LR P-value: 2.46E-15;
mr1680_2 (All); LR P-value: 2.34E-10;
mr1877_2 (All); LR P-value: 5.18E-22;
mr1950_2 (All); LR P-value: 1.54E-14;
mr1971_2 (All); LR P-value: 1.21E-23
LOC_Os06g20010.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 72.931; most accessible tissue: Zhenshan97 young leaf, score: 90.728
vg0611474667 (J) chr06 11474667 C T 98.90% 0.00% C -> T NA
LOC_Os06g20010.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 73.135; most accessible tissue: Zhenshan97 young leaf, score: 90.901
vg0611474672 (J) chr06 11474672 C T 98.10% 0.00% C -> T NA
LOC_Os06g20010.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 73.256; most accessible tissue: Zhenshan97 young leaf, score: 90.728
vg0611474683 (J) chr06 11474683 G A 99.30% 0.00% G -> A NA
LOC_Os06g20010.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os06g20000.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os06g20020.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 74.631; most accessible tissue: Zhenshan97 young leaf, score: 90.456
vg0611474689 (J) chr06 11474689 G A 52.10% 0.08% G -> A
mr1037 (All); LR P-value: 4.07E-28;
mr1065 (All); LMM P-value: 3.45E-08; LR P-value: 7.71E-70;
mr1065 (Ind_All); LR P-value: 1.23E-11;
mr1067 (All); LR P-value: 1.04E-47;
mr1068 (All); LMM P-value: 1.01E-08; LR P-value: 1.99E-69;
mr1068 (Ind_All); LMM P-value: 2.63E-06; LR P-value: 5.34E-12;
mr1078 (All); LMM P-value: 6.37E-07; LR P-value: 9.56E-61;
mr1078 (Ind_All); LR P-value: 2.09E-08;
mr1087 (All); LMM P-value: 7.62E-08; LR P-value: 4.09E-64;
mr1087 (Ind_All); LR P-value: 1.16E-09;
mr1090 (All); LMM P-value: 5.94E-07; LR P-value: 9.74E-61;
mr1090 (Ind_All); LMM P-value: 6.90E-06; LR P-value: 2.30E-07;
mr1091 (All); LMM P-value: 1.40E-07; LR P-value: 7.04E-50;
mr1091 (Ind_All); LR P-value: 3.64E-10;
mr1094 (All); LMM P-value: 5.51E-07; LR P-value: 1.13E-46;
mr1094 (Ind_All); LR P-value: 7.13E-07;
mr1096 (All); LMM P-value: 4.91E-06; LR P-value: 5.93E-60;
mr1096 (Ind_All); LR P-value: 2.53E-07;
mr1108 (All); LMM P-value: 3.69E-06; LR P-value: 9.24E-56;
mr1108 (Ind_All); LR P-value: 4.15E-10;
mr1110 (All); LR P-value: 3.16E-44;
mr1111 (All); LR P-value: 8.48E-57;
mr1111 (Ind_All); LR P-value: 7.36E-09;
mr1112 (All); LR P-value: 3.78E-55;
mr1112 (Ind_All); LR P-value: 1.26E-08;
mr1121 (All); LMM P-value: 1.83E-07; LR P-value: 1.61E-59;
mr1121 (Ind_All); LMM P-value: 7.06E-06; LR P-value: 3.24E-09;
mr1131 (All); LR P-value: 2.13E-21;
mr1144 (All); LMM P-value: 1.05E-07; LR P-value: 8.32E-58;
mr1144 (Ind_All); LMM P-value: 6.09E-06; LR P-value: 1.03E-10;
mr1200 (All); LR P-value: 8.03E-51;
mr1200 (Ind_All); LR P-value: 4.75E-08;
mr1211 (All); LMM P-value: 9.41E-06; LR P-value: 2.18E-54;
mr1211 (Ind_All); LR P-value: 3.75E-06;
mr1234 (All); LR P-value: 6.42E-53;
mr1237 (All); LR P-value: 1.16E-37;
mr1237 (Ind_All); LR P-value: 1.21E-07;
mr1270 (All); LR P-value: 4.70E-13;
mr1426 (All); LR P-value: 2.65E-29;
mr1526 (All); LR P-value: 4.31E-49;
mr1526 (Ind_All); LR P-value: 5.17E-08;
mr1877 (All); LR P-value: 5.41E-30;
mr1878 (All); LR P-value: 7.69E-33;
mr1065_2 (All); LMM P-value: 3.35E-06; LR P-value: 1.95E-77;
mr1065_2 (Ind_All); LMM P-value: 6.34E-07; LR P-value: 1.83E-14;
mr1067_2 (All); LR P-value: 1.62E-60;
mr1067_2 (Ind_All); LR P-value: 1.80E-10;
mr1068_2 (All); LMM P-value: 7.48E-08; LR P-value: 7.37E-82;
mr1068_2 (Ind_All); LMM P-value: 5.20E-08; LR P-value: 2.97E-15;
mr1078_2 (All); LMM P-value: 6.62E-06; LR P-value: 5.68E-73;
mr1078_2 (Ind_All); LR P-value: 5.22E-10;
mr1087_2 (All); LMM P-value: 1.79E-08; LR P-value: 2.09E-75;
mr1087_2 (Ind_All); LMM P-value: 4.51E-08; LR P-value: 2.39E-13;
mr1090_2 (All); LMM P-value: 6.19E-06; LR P-value: 9.43E-67;
mr1090_2 (Ind_All); LMM P-value: 4.25E-07; LR P-value: 9.36E-09;
mr1091_2 (All); LMM P-value: 1.28E-06; LR P-value: 6.80E-61;
mr1091_2 (Ind_All); LMM P-value: 7.33E-06; LR P-value: 1.16E-11;
mr1094_2 (All); LR P-value: 3.45E-54;
mr1094_2 (Ind_All); LR P-value: 5.39E-08;
mr1096_2 (All); LR P-value: 7.27E-69;
mr1096_2 (Ind_All); LR P-value: 5.33E-10;
mr1108_2 (All); LMM P-value: 1.55E-06; LR P-value: 9.01E-66;
mr1108_2 (Ind_All); LMM P-value: 1.48E-06; LR P-value: 3.69E-12;
mr1110_2 (All); LMM P-value: 9.58E-06; LR P-value: 2.41E-48;
mr1110_2 (Ind_All); LR P-value: 2.37E-08;
mr1111_2 (All); LMM P-value: 2.06E-07; LR P-value: 2.93E-64;
mr1111_2 (Ind_All); LMM P-value: 3.07E-09; LR P-value: 7.37E-14;
mr1112_2 (All); LMM P-value: 1.45E-06; LR P-value: 7.26E-74;
mr1112_2 (Ind_All); LMM P-value: 4.84E-06; LR P-value: 1.59E-12;
mr1121_2 (All); LR P-value: 4.63E-59;
mr1121_2 (Ind_All); LR P-value: 4.46E-09;
mr1131_2 (All); LR P-value: 3.50E-18;
mr1144_2 (All); LMM P-value: 6.73E-06; LR P-value: 4.78E-63;
mr1144_2 (Ind_All); LMM P-value: 3.05E-06; LR P-value: 2.16E-11;
mr1199_2 (All); LR P-value: 3.01E-17;
mr1200_2 (All); LR P-value: 2.96E-61;
mr1200_2 (Ind_All); LMM P-value: 3.38E-06; LR P-value: 2.73E-11;
mr1211_2 (All); LMM P-value: 5.48E-07; LR P-value: 4.48E-63;
mr1211_2 (Ind_All); LMM P-value: 5.09E-07; LR P-value: 1.53E-09;
mr1221_2 (All); LR P-value: 5.73E-34;
mr1234_2 (All); LR P-value: 1.64E-68;
mr1234_2 (Ind_All); LR P-value: 1.19E-11;
mr1341_2 (All); LR P-value: 6.71E-06;
mr1526_2 (All); LMM P-value: 1.86E-06; LR P-value: 5.22E-64;
mr1526_2 (Ind_All); LMM P-value: 1.41E-07; LR P-value: 1.90E-13;
mr1686_2 (All); LR P-value: 3.65E-15;
mr1690_2 (All); LR P-value: 2.15E-08;
mr1877_2 (All); LR P-value: 4.70E-24
LOC_Os06g20010.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g20010.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 74.714; most accessible tissue: Zhenshan97 young leaf, score: 90.547
vg0611474705 (J) chr06 11474705 A G 54.00% 0.00% G -> A
mr1020 (Jap_All); LMM P-value: 4.62E-06; LR P-value: 2.69E-06;
mr1053 (All); LR P-value: 1.15E-07;
mr1058 (All); LR P-value: 3.09E-06;
mr1065 (All); LMM P-value: 1.39E-06; LR P-value: 1.21E-59;
mr1065 (Ind_All); LMM P-value: 5.83E-07; LR P-value: 1.77E-11;
mr1068 (All); LR P-value: 7.82E-59;
mr1068 (Ind_All); LMM P-value: 7.79E-07; LR P-value: 8.46E-11;
mr1078 (All); LR P-value: 1.89E-50;
mr1078 (Ind_All); LR P-value: 5.54E-09;
mr1087 (All); LMM P-value: 2.19E-08; LR P-value: 1.68E-64;
mr1087 (Ind_All); LMM P-value: 2.78E-07; LR P-value: 5.44E-11;
mr1089 (All); LR P-value: 2.74E-41;
mr1090 (All); LMM P-value: 7.80E-06; LR P-value: 2.42E-55;
mr1090 (Ind_All); LMM P-value: 5.52E-07; LR P-value: 2.81E-07;
mr1091 (All); LMM P-value: 1.61E-07; LR P-value: 2.93E-43;
mr1091 (Ind_All); LMM P-value: 2.09E-06; LR P-value: 1.34E-09;
mr1094 (All); LMM P-value: 2.26E-06; LR P-value: 2.75E-42;
mr1096 (All); LMM P-value: 1.20E-06; LR P-value: 1.74E-56;
mr1096 (Ind_All); LR P-value: 2.75E-08;
mr1108 (All); LMM P-value: 1.32E-06; LR P-value: 1.62E-51;
mr1108 (Ind_All); LR P-value: 1.28E-09;
mr1110 (All); LR P-value: 1.47E-43;
mr1111 (All); LR P-value: 7.19E-48;
mr1111 (Ind_All); LR P-value: 1.39E-07;
mr1112 (All); LMM P-value: 7.19E-07; LR P-value: 1.35E-52;
mr1112 (Ind_All); LR P-value: 5.06E-09;
mr1121 (All); LMM P-value: 3.61E-07; LR P-value: 7.65E-56;
mr1121 (Ind_All); LMM P-value: 9.26E-08; LR P-value: 2.66E-10;
mr1131 (All); LR P-value: 7.94E-20;
mr1138 (All); LR P-value: 2.47E-12;
mr1139 (All); LR P-value: 1.01E-38;
mr1144 (All); LMM P-value: 3.65E-07; LR P-value: 2.15E-51;
mr1144 (Ind_All); LMM P-value: 1.12E-06; LR P-value: 3.33E-10;
mr1145 (All); LR P-value: 2.66E-28;
mr1147 (All); LR P-value: 5.91E-18;
mr1165 (Jap_All); LMM P-value: 5.35E-06; LR P-value: 5.35E-06;
mr1200 (All); LR P-value: 2.79E-41;
mr1200 (Ind_All); LR P-value: 9.28E-08;
mr1211 (All); LR P-value: 4.25E-50;
mr1211 (Ind_All); LR P-value: 8.51E-07;
mr1237 (All); LR P-value: 2.06E-31;
mr1478 (Jap_All); LMM P-value: 1.30E-08; LR P-value: 1.30E-08;
mr1526 (All); LR P-value: 4.16E-46;
mr1526 (Ind_All); LR P-value: 4.71E-09;
mr1745 (All); LR P-value: 4.77E-31;
mr1763 (All); LR P-value: 3.08E-08;
mr1877 (All); LR P-value: 6.08E-29;
mr1878 (All); LR P-value: 1.16E-31;
mr1971 (Jap_All); LMM P-value: 5.00E-07; LR P-value: 3.37E-08;
mr1065_2 (All); LMM P-value: 1.94E-06; LR P-value: 5.66E-67;
mr1065_2 (Ind_All); LMM P-value: 4.65E-09; LR P-value: 6.22E-15;
mr1068_2 (All); LMM P-value: 5.27E-07; LR P-value: 5.96E-72;
mr1068_2 (Ind_All); LMM P-value: 2.36E-09; LR P-value: 2.36E-15;
mr1078_2 (All); LR P-value: 6.22E-62;
mr1078_2 (Ind_All); LMM P-value: 8.16E-06; LR P-value: 1.06E-09;
mr1087_2 (All); LMM P-value: 5.37E-08; LR P-value: 9.41E-73;
mr1087_2 (Ind_All); LMM P-value: 6.79E-10; LR P-value: 3.05E-14;
mr1090_2 (All); LR P-value: 7.17E-62;
mr1090_2 (Ind_All); LMM P-value: 1.02E-08; LR P-value: 1.84E-09;
mr1091_2 (All); LMM P-value: 4.94E-08; LR P-value: 6.37E-56;
mr1091_2 (Ind_All); LMM P-value: 1.27E-07; LR P-value: 3.13E-11;
mr1094_2 (All); LMM P-value: 4.40E-06; LR P-value: 1.47E-51;
mr1094_2 (Ind_All); LR P-value: 1.02E-07;
mr1096_2 (All); LMM P-value: 1.61E-06; LR P-value: 9.52E-65;
mr1096_2 (Ind_All); LMM P-value: 1.20E-07; LR P-value: 4.26E-11;
mr1108_2 (All); LMM P-value: 5.95E-07; LR P-value: 5.36E-59;
mr1108_2 (Ind_All); LMM P-value: 3.00E-08; LR P-value: 1.05E-12;
mr1110_2 (All); LR P-value: 3.72E-46;
mr1110_2 (Ind_All); LR P-value: 2.27E-08;
mr1111_2 (All); LMM P-value: 2.89E-06; LR P-value: 1.79E-53;
mr1111_2 (Ind_All); LMM P-value: 1.03E-10; LR P-value: 8.26E-14;
mr1112_2 (All); LMM P-value: 1.52E-08; LR P-value: 1.56E-71;
mr1112_2 (Ind_All); LMM P-value: 5.08E-08; LR P-value: 2.65E-13;
mr1121_2 (All); LR P-value: 5.35E-56;
mr1121_2 (Ind_All); LMM P-value: 2.99E-06; LR P-value: 2.51E-09;
mr1144_2 (All); LR P-value: 4.89E-54;
mr1144_2 (Ind_All); LMM P-value: 1.70E-07; LR P-value: 4.73E-11;
mr1165_2 (Jap_All); LMM P-value: 2.25E-07; LR P-value: 3.14E-09;
mr1200_2 (All); LR P-value: 2.58E-55;
mr1200_2 (Ind_All); LMM P-value: 8.15E-08; LR P-value: 1.19E-12;
mr1211_2 (All); LR P-value: 2.96E-55;
mr1211_2 (Ind_All); LMM P-value: 1.24E-07; LR P-value: 1.54E-09;
mr1234_2 (All); LMM P-value: 8.66E-06; LR P-value: 4.36E-60;
mr1234_2 (Ind_All); LMM P-value: 1.46E-06; LR P-value: 7.96E-11;
mr1325_2 (All); LR P-value: 2.42E-12;
mr1477_2 (Jap_All); LMM P-value: 6.94E-07; LR P-value: 6.95E-07;
mr1526_2 (All); LR P-value: 8.30E-60;
mr1526_2 (Ind_All); LMM P-value: 3.15E-07; LR P-value: 9.91E-11;
mr1527_2 (All); LR P-value: 2.56E-07;
mr1649_2 (All); LR P-value: 1.48E-09;
mr1690_2 (All); LR P-value: 4.96E-08;
mr1877_2 (All); LR P-value: 1.20E-24
LOC_Os06g20010.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 75.898; most accessible tissue: Zhenshan97 young leaf, score: 90.815
vg0611474740 (J) chr06 11474740 C T 95.10% 0.00% C -> T NA
LOC_Os06g20010.1 Alt: T| start_lost HIGH(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 75.668; most accessible tissue: Zhenshan97 young leaf, score: 90.456