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Search Results:

24 variations found. Os12g0135200/LOC_Os12g04130 (OsFBO23 - F-box and other domain containing protein; expressed), ranging from 1,732,194 bp to 1,734,982 bp (including 0 kb upstream and 0 kb downstream of the gene).

Gene IDAnnotation
LOC_Os12g04130 OsFBO23 - F-box and other domain containing protein; RAP ID: Os12g0135200; MSU ID: LOC_Os12g04130

Gene Expression Atlas:

The expression data is from the CREP database. And the expression value is log2-transformed. Move the mouse over the cells of the heat map to get detailed tissue information and expression values.

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
vg1201732244 (J) chr12 1732244 T C 99.80% 0.00% T -> C NA
LOC_Os12g04130.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os12g04120.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 91.694; most accessible tissue: Zhenshan97 panicle, score: 98.386
vg1201732336 (J) chr12 1732336 A C 98.50% 0.19% A -> C NA
LOC_Os12g04130.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os12g04130.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 87.834; most accessible tissue: Zhenshan97 panicle, score: 98.337
vg1201732355 (J) chr12 1732355 C T 64.70% 0.00% T -> C NA
LOC_Os12g04130.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 85.850; most accessible tissue: Zhenshan97 panicle, score: 97.816
vg1201732589 (J) chr12 1732589 T C 56.70% 0.00% C -> T NA
LOC_Os12g04130.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 82.500; most accessible tissue: Zhenshan97 panicle, score: 96.335
vg1201732728 (J) chr12 1732728 T G 56.80% 0.00% G -> T NA
LOC_Os12g04130.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 86.706; most accessible tissue: Zhenshan97 panicle, score: 97.445
vg1201732801 (J) chr12 1732801 G T 92.10% 0.34% G -> T NA
LOC_Os12g04130.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g04130.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 86.438; most accessible tissue: Zhenshan97 panicle, score: 97.303
vg1201732991 (J) chr12 1732991 C T 69.70% 10.37% C -> T NA
LOC_Os12g04130.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g04130.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 88.246; most accessible tissue: Zhenshan97 panicle, score: 97.869
vg1201733206 (J) chr12 1733206 G A 82.60% 0.00% G -> A
mr1042 (Ind_All); LR P-value: 9.94E-06;
mr1043 (Ind_All); LR P-value: 3.12E-06;
mr1155 (Ind_All); LR P-value: 7.01E-06;
mr1354 (Ind_All); LR P-value: 1.78E-06;
mr1399 (Ind_All); LR P-value: 5.87E-07;
mr1502 (Ind_All); LR P-value: 1.83E-06;
mr1535 (Ind_All); LR P-value: 5.91E-09;
mr1677 (Ind_All); LR P-value: 2.42E-06;
mr1896 (Ind_All); LR P-value: 6.82E-09;
mr1912 (Ind_All); LR P-value: 4.68E-06;
mr1935 (Ind_All); LR P-value: 1.42E-09;
mr1974 (All); LR P-value: 2.59E-06
LOC_Os12g04130.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 89.764; most accessible tissue: Zhenshan97 panicle, score: 98.145
vg1201733259 (J) chr12 1733259 T G 98.30% 0.19% T -> G NA
LOC_Os12g04130.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g04130.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 89.820; most accessible tissue: Zhenshan97 panicle, score: 98.006
vg1201733332 (J) chr12 1733332 C T 99.40% 0.00% C -> T NA
LOC_Os12g04130.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os12g04120.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 88.641; most accessible tissue: Zhenshan97 panicle, score: 98.244
vg1201733502 (J) chr12 1733502 G T 99.80% 0.00% G -> T NA
LOC_Os12g04130.1 Alt: T| splice_region_variant&intron_variant LOW(snpEff)
LOC_Os12g04120.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 92.135; most accessible tissue: Zhenshan97 panicle, score: 97.121
vg1201733519 (J) chr12 1733519 A T 92.60% 0.00% A -> T
mr1153 (All); LR P-value: 3.59E-06;
mr1305 (All); LR P-value: 1.57E-24;
mr1365 (All); LR P-value: 1.51E-07;
mr1515 (All); LR P-value: 1.63E-19;
mr1556 (All); LR P-value: 3.74E-07;
mr1586 (All); LR P-value: 1.39E-28;
mr1649 (All); LR P-value: 8.08E-12;
mr1764 (All); LR P-value: 4.05E-08;
mr1808 (All); LR P-value: 5.92E-06;
mr1344_2 (All); LR P-value: 8.05E-06;
mr1409_2 (All); LR P-value: 1.22E-11;
mr1803_2 (All); LR P-value: 6.01E-12;
mr1808_2 (All); LR P-value: 4.86E-07;
mr1815_2 (All); LR P-value: 5.68E-07
LOC_Os12g04120.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g04130.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 91.446; most accessible tissue: Zhenshan97 panicle, score: 96.801
vg1201733799 (J) chr12 1733799 G A 99.80% 0.00% G -> A NA
LOC_Os12g04120.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os12g04130.1 Alt: A| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 85.877; most accessible tissue: Callus, score: 97.684
vg1201734025 (J) chr12 1734025 A T 64.60% 0.00% T -> A
mr1074 (All); LR P-value: 1.00E-31;
mr1081 (All); LR P-value: 4.83E-34;
mr1130 (All); LR P-value: 9.66E-26;
mr1148 (All); LR P-value: 3.93E-29;
mr1256 (All); LR P-value: 8.86E-31;
mr1307 (All); LR P-value: 3.89E-10;
mr1414 (All); LR P-value: 5.46E-28;
mr1542 (All); LR P-value: 2.58E-35;
mr1645 (All); LR P-value: 8.44E-39;
mr1681 (All); LR P-value: 6.95E-06;
mr1686 (All); LR P-value: 3.40E-26;
mr1711 (All); LR P-value: 4.27E-59;
mr1767 (All); LR P-value: 6.61E-18;
mr1776 (All); LR P-value: 1.58E-08;
mr1810 (All); LR P-value: 2.76E-07;
mr1924 (All); LR P-value: 2.99E-13;
mr1979 (All); LR P-value: 6.73E-07;
mr1082_2 (All); LR P-value: 1.78E-36;
mr1085_2 (All); LR P-value: 6.08E-32;
mr1103_2 (All); LR P-value: 2.01E-66;
mr1238_2 (All); LR P-value: 1.86E-28;
mr1264_2 (All); LR P-value: 1.89E-39;
mr1403_2 (All); LR P-value: 5.53E-25;
mr1609_2 (All); LR P-value: 5.76E-22;
mr1841_2 (All); LR P-value: 6.09E-33;
mr1900_2 (All); LR P-value: 3.61E-21;
mr1915_2 (All); LR P-value: 3.03E-06
LOC_Os12g04130.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 86.504; most accessible tissue: Callus, score: 96.776
vg1201734131 (J) chr12 1734131 T A 56.90% 0.00% A -> T
mr1026 (All); LR P-value: 2.50E-32;
mr1063 (All); LR P-value: 9.47E-48;
mr1083 (All); LR P-value: 1.79E-22;
mr1088 (All); LR P-value: 6.90E-58;
mr1145 (All); LR P-value: 4.79E-28;
mr1224 (All); LR P-value: 1.14E-31;
mr1225 (All); LR P-value: 1.01E-30;
mr1226 (All); LR P-value: 2.05E-28;
mr1233 (All); LR P-value: 1.36E-11;
mr1246 (All); LR P-value: 2.77E-63;
mr1342 (All); LR P-value: 1.83E-09;
mr1560 (All); LR P-value: 3.13E-30;
mr1047_2 (All); LR P-value: 3.26E-10;
mr1088_2 (All); LR P-value: 1.10E-75;
mr1112_2 (All); LR P-value: 6.34E-61;
mr1121_2 (All); LR P-value: 6.93E-51;
mr1189_2 (All); LR P-value: 1.92E-13;
mr1224_2 (All); LR P-value: 3.00E-37;
mr1246_2 (All); LR P-value: 3.11E-79;
mr1264_2 (All); LR P-value: 2.19E-38;
mr1270_2 (All); LR P-value: 5.10E-28;
mr1404_2 (All); LR P-value: 2.11E-50;
mr1623_2 (All); LR P-value: 4.09E-07;
mr1734_2 (All); LR P-value: 7.06E-12;
mr1744_2 (All); LR P-value: 2.96E-16;
mr1782_2 (All); LR P-value: 1.88E-11;
mr1834_2 (All); LR P-value: 2.44E-06;
mr1973_2 (All); LR P-value: 2.45E-95
LOC_Os12g04120.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g04130.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 81.224; most accessible tissue: Zhenshan97 flower, score: 93.553
vg1201734184 (J) chr12 1734184 C G 56.80% 0.00% G -> C
mr1026 (All); LR P-value: 7.65E-33;
mr1063 (All); LR P-value: 7.07E-48;
mr1076 (Ind_All); LR P-value: 2.42E-06;
mr1082 (Ind_All); LR P-value: 7.30E-08;
mr1083 (All); LR P-value: 4.87E-22;
mr1083 (Ind_All); LR P-value: 5.51E-06;
mr1085 (Ind_All); LR P-value: 8.80E-06;
mr1086 (Ind_All); LR P-value: 1.09E-06;
mr1088 (All); LR P-value: 1.22E-57;
mr1088 (Ind_All); LR P-value: 1.02E-07;
mr1103 (Ind_All); LR P-value: 2.40E-08;
mr1104 (Ind_All); LR P-value: 5.31E-09;
mr1107 (Ind_All); LR P-value: 5.64E-09;
mr1139 (Ind_All); LR P-value: 3.86E-08;
mr1145 (All); LR P-value: 1.01E-27;
mr1145 (Ind_All); LR P-value: 5.13E-07;
mr1161 (All); LR P-value: 2.38E-32;
mr1204 (All); LR P-value: 1.09E-29;
mr1204 (Ind_All); LR P-value: 2.14E-06;
mr1224 (All); LR P-value: 3.30E-31;
mr1225 (All); LR P-value: 2.12E-31;
mr1226 (Ind_All); LR P-value: 2.24E-11;
mr1227 (Ind_All); LR P-value: 9.09E-06;
mr1233 (All); LR P-value: 2.47E-11;
mr1237 (All); LR P-value: 4.25E-29;
mr1246 (All); LR P-value: 4.70E-63;
mr1246 (Ind_All); LR P-value: 3.46E-06;
mr1342 (All); LR P-value: 3.58E-09;
mr1411 (Ind_All); LR P-value: 5.23E-11;
mr1436 (Ind_All); LR P-value: 3.34E-06;
mr1437 (Ind_All); LR P-value: 3.97E-10;
mr1560 (All); LR P-value: 6.81E-30;
mr1560 (Ind_All); LR P-value: 8.65E-11;
mr1878 (Ind_All); LR P-value: 6.39E-06;
mr1949 (Ind_All); LR P-value: 2.42E-06;
mr1973 (All); LR P-value: 8.76E-79;
mr1070_2 (Ind_All); LR P-value: 1.06E-10;
mr1088_2 (All); LR P-value: 1.31E-74;
mr1088_2 (Ind_All); LR P-value: 7.94E-08;
mr1111_2 (All); LR P-value: 7.39E-49;
mr1112_2 (All); LR P-value: 1.23E-60;
mr1121_2 (All); LR P-value: 2.89E-51;
mr1189_2 (All); LR P-value: 8.35E-13;
mr1224_2 (All); LR P-value: 7.14E-37;
mr1246_2 (All); LR P-value: 5.02E-78;
mr1246_2 (Ind_All); LR P-value: 1.15E-07;
mr1264_2 (Ind_All); LR P-value: 7.76E-07;
mr1270_2 (All); LR P-value: 1.73E-27;
mr1404_2 (Ind_All); LR P-value: 1.39E-06;
mr1437_2 (Ind_All); LR P-value: 2.00E-10;
mr1620_2 (Ind_All); LR P-value: 4.71E-07;
mr1623_2 (All); LR P-value: 6.51E-07;
mr1734_2 (All); LR P-value: 2.39E-11;
mr1744_2 (All); LR P-value: 7.80E-16;
mr1782_2 (All); LR P-value: 2.51E-10;
mr1878_2 (Ind_All); LR P-value: 1.57E-07;
mr1949_2 (Ind_All); LR P-value: 1.20E-07;
mr1973_2 (All); LR P-value: 1.69E-96
LOC_Os12g04120.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g04130.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 84.105; most accessible tissue: Zhenshan97 flower, score: 93.734
vg1201734303 (J) chr12 1734303 A G 64.60% 0.00% G -> A
mr1074 (All); LR P-value: 1.00E-31;
mr1081 (All); LR P-value: 4.83E-34;
mr1130 (All); LR P-value: 9.66E-26;
mr1148 (All); LR P-value: 3.93E-29;
mr1256 (All); LR P-value: 8.86E-31;
mr1307 (All); LR P-value: 3.89E-10;
mr1414 (All); LR P-value: 5.46E-28;
mr1542 (All); LR P-value: 2.58E-35;
mr1645 (All); LR P-value: 8.44E-39;
mr1681 (All); LR P-value: 6.95E-06;
mr1686 (All); LR P-value: 3.40E-26;
mr1711 (All); LR P-value: 4.27E-59;
mr1767 (All); LR P-value: 6.61E-18;
mr1776 (All); LR P-value: 1.58E-08;
mr1810 (All); LR P-value: 2.76E-07;
mr1924 (All); LR P-value: 2.99E-13;
mr1979 (All); LR P-value: 6.73E-07;
mr1082_2 (All); LR P-value: 1.78E-36;
mr1085_2 (All); LR P-value: 6.08E-32;
mr1103_2 (All); LR P-value: 2.01E-66;
mr1238_2 (All); LR P-value: 1.86E-28;
mr1264_2 (All); LR P-value: 1.89E-39;
mr1403_2 (All); LR P-value: 5.53E-25;
mr1609_2 (All); LR P-value: 5.76E-22;
mr1841_2 (All); LR P-value: 6.09E-33;
mr1900_2 (All); LR P-value: 3.61E-21;
mr1915_2 (All); LR P-value: 3.03E-06
LOC_Os12g04130.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 86.036; most accessible tissue: Zhenshan97 flower, score: 93.774
vg1201734706 (J) chr12 1734706 C T 64.60% 0.00% T -> C
mr1074 (All); LR P-value: 1.00E-31;
mr1081 (All); LR P-value: 4.83E-34;
mr1130 (All); LR P-value: 9.66E-26;
mr1148 (All); LR P-value: 3.93E-29;
mr1256 (All); LR P-value: 8.86E-31;
mr1307 (All); LR P-value: 3.89E-10;
mr1414 (All); LR P-value: 5.46E-28;
mr1542 (All); LR P-value: 2.58E-35;
mr1645 (All); LR P-value: 8.44E-39;
mr1681 (All); LR P-value: 6.95E-06;
mr1686 (All); LR P-value: 3.40E-26;
mr1711 (All); LR P-value: 4.27E-59;
mr1767 (All); LR P-value: 6.61E-18;
mr1776 (All); LR P-value: 1.58E-08;
mr1810 (All); LR P-value: 2.76E-07;
mr1924 (All); LR P-value: 2.99E-13;
mr1979 (All); LR P-value: 6.73E-07;
mr1082_2 (All); LR P-value: 1.78E-36;
mr1085_2 (All); LR P-value: 6.08E-32;
mr1103_2 (All); LR P-value: 2.01E-66;
mr1238_2 (All); LR P-value: 1.86E-28;
mr1264_2 (All); LR P-value: 1.89E-39;
mr1403_2 (All); LR P-value: 5.53E-25;
mr1609_2 (All); LR P-value: 5.76E-22;
mr1841_2 (All); LR P-value: 6.09E-33;
mr1900_2 (All); LR P-value: 3.61E-21;
mr1915_2 (All); LR P-value: 3.03E-06
LOC_Os12g04130.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 81.991; most accessible tissue: Zhenshan97 panicle, score: 93.133
vg1201734715 (J) chr12 1734715 T C 56.60% 0.00% C -> T
mr1026 (All); LR P-value: 1.66E-32;
mr1063 (All); LR P-value: 4.08E-49;
mr1083 (All); LR P-value: 3.24E-22;
mr1088 (All); LR P-value: 1.87E-58;
mr1108 (All); LR P-value: 7.60E-44;
mr1145 (All); LR P-value: 8.67E-28;
mr1161 (All); LR P-value: 1.59E-32;
mr1204 (All); LR P-value: 1.29E-29;
mr1224 (All); LR P-value: 1.59E-32;
mr1225 (All); LR P-value: 1.58E-31;
mr1233 (All); LR P-value: 1.95E-11;
mr1237 (All); LR P-value: 2.14E-29;
mr1246 (All); LR P-value: 1.77E-63;
mr1342 (All); LR P-value: 3.81E-09;
mr1437 (All); LR P-value: 3.20E-39;
mr1560 (All); LR P-value: 6.24E-30;
mr1878 (All); LR P-value: 1.34E-31;
mr1088_2 (All); LR P-value: 2.01E-76;
mr1108_2 (All); LR P-value: 8.92E-54;
mr1111_2 (All); LR P-value: 1.79E-49;
mr1112_2 (All); LR P-value: 1.05E-61;
mr1121_2 (All); LR P-value: 4.54E-52;
mr1144_2 (All); LR P-value: 4.45E-50;
mr1189_2 (All); LR P-value: 5.19E-13;
mr1224_2 (All); LR P-value: 6.62E-38;
mr1246_2 (All); LR P-value: 1.95E-80;
mr1264_2 (All); LR P-value: 1.80E-38;
mr1270_2 (All); LR P-value: 1.27E-28;
mr1404_2 (All); LR P-value: 2.92E-50;
mr1559_2 (All); LR P-value: 3.14E-06;
mr1623_2 (All); LR P-value: 7.49E-07;
mr1734_2 (All); LR P-value: 1.43E-11;
mr1744_2 (All); LR P-value: 2.98E-16;
mr1782_2 (All); LR P-value: 5.50E-11;
mr1973_2 (All); LR P-value: 3.61E-95
LOC_Os12g04130.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 81.567; most accessible tissue: Zhenshan97 panicle, score: 92.660
vg1201734781 (J) chr12 1734781 G C 99.40% 0.00% G -> C NA
LOC_Os12g04130.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 79.407; most accessible tissue: Zhenshan97 panicle, score: 92.133
vg1201734838 (J) chr12 1734838 C G 56.70% 0.00% G -> C
mr1026 (All); LR P-value: 3.43E-33;
mr1063 (All); LR P-value: 3.95E-48;
mr1083 (All); LR P-value: 1.60E-22;
mr1088 (All); LR P-value: 2.66E-58;
mr1145 (All); LR P-value: 4.09E-28;
mr1161 (All); LR P-value: 6.22E-33;
mr1224 (All); LR P-value: 3.45E-32;
mr1225 (All); LR P-value: 2.25E-31;
mr1226 (All); LR P-value: 2.36E-28;
mr1233 (All); LR P-value: 1.56E-11;
mr1246 (All); LR P-value: 6.41E-64;
mr1342 (All); LR P-value: 2.89E-09;
mr1560 (All); LR P-value: 4.18E-30;
mr1878 (All); LR P-value: 2.14E-31;
mr1047_2 (All); LR P-value: 6.70E-10;
mr1088_2 (All); LR P-value: 4.05E-76;
mr1111_2 (All); LR P-value: 6.98E-49;
mr1112_2 (All); LR P-value: 1.16E-60;
mr1121_2 (All); LR P-value: 3.21E-51;
mr1189_2 (All); LR P-value: 3.11E-13;
mr1224_2 (All); LR P-value: 7.53E-38;
mr1246_2 (All); LR P-value: 1.15E-79;
mr1264_2 (All); LR P-value: 1.80E-38;
mr1270_2 (All); LR P-value: 3.97E-28;
mr1404_2 (All); LR P-value: 3.31E-50;
mr1623_2 (All); LR P-value: 3.65E-07;
mr1734_2 (All); LR P-value: 8.45E-12;
mr1744_2 (All); LR P-value: 2.98E-16;
mr1782_2 (All); LR P-value: 3.86E-11
LOC_Os12g04130.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 73.377; most accessible tissue: Zhenshan97 panicle, score: 90.061
vg1201734867 (J) chr12 1734867 C T 56.60% 0.00% T -> C
mr1026 (All); LR P-value: 3.88E-32;
mr1076 (Ind_All); LR P-value: 2.32E-07;
mr1082 (Ind_All); LR P-value: 2.42E-07;
mr1083 (All); LR P-value: 8.95E-23;
mr1083 (Ind_All); LR P-value: 4.57E-07;
mr1086 (Ind_All); LR P-value: 3.80E-07;
mr1088 (All); LR P-value: 2.10E-57;
mr1088 (Ind_All); LR P-value: 1.30E-07;
mr1103 (Ind_All); LR P-value: 3.22E-09;
mr1104 (Ind_All); LR P-value: 2.95E-09;
mr1107 (Ind_All); LR P-value: 9.14E-09;
mr1139 (All); LR P-value: 9.72E-39;
mr1139 (Ind_All); LR P-value: 2.24E-09;
mr1145 (All); LR P-value: 1.29E-28;
mr1145 (Ind_All); LR P-value: 3.20E-08;
mr1204 (All); LR P-value: 1.24E-29;
mr1204 (Ind_All); LR P-value: 2.63E-06;
mr1224 (All); LR P-value: 2.03E-32;
mr1224 (Ind_All); LR P-value: 4.02E-06;
mr1225 (All); LR P-value: 1.98E-32;
mr1225 (Ind_All); LR P-value: 3.28E-06;
mr1226 (Ind_All); LR P-value: 3.22E-11;
mr1233 (All); LR P-value: 1.86E-11;
mr1246 (All); LR P-value: 7.44E-63;
mr1246 (Ind_All); LR P-value: 3.39E-06;
mr1342 (All); LR P-value: 1.90E-09;
mr1411 (Ind_All); LR P-value: 8.39E-12;
mr1436 (All); LR P-value: 2.39E-29;
mr1436 (Ind_All); LR P-value: 1.92E-08;
mr1437 (All); LR P-value: 1.72E-39;
mr1437 (Ind_All); LR P-value: 1.15E-10;
mr1560 (All); LR P-value: 3.53E-30;
mr1560 (Ind_All); LR P-value: 3.49E-11;
mr1620 (Ind_All); LR P-value: 4.96E-06;
mr1878 (All); LR P-value: 2.58E-32;
mr1878 (Ind_All); LR P-value: 1.40E-07;
mr1949 (Ind_All); LR P-value: 9.08E-07;
mr1070_2 (Ind_All); LR P-value: 3.14E-11;
mr1076_2 (Ind_All); LMM P-value: 2.35E-06; LR P-value: 6.45E-13;
mr1082_2 (Ind_All); LMM P-value: 5.95E-06;
mr1083_2 (Ind_All); LMM P-value: 1.72E-06;
mr1085_2 (Ind_All); LMM P-value: 7.92E-07; LR P-value: 3.61E-12;
mr1088_2 (All); LR P-value: 1.13E-74;
mr1088_2 (Ind_All); LR P-value: 3.11E-08;
mr1121_2 (All); LR P-value: 2.64E-51;
mr1147_2 (All); LR P-value: 1.45E-12;
mr1189_2 (All); LR P-value: 5.47E-13;
mr1199_2 (All); LR P-value: 2.88E-17;
mr1199_2 (Ind_All); LR P-value: 6.94E-06;
mr1208_2 (All); LR P-value: 3.60E-37;
mr1224_2 (All); LR P-value: 2.52E-38;
mr1224_2 (Ind_All); LR P-value: 8.01E-07;
mr1227_2 (Ind_All); LR P-value: 2.87E-06;
mr1233_2 (Ind_All); LR P-value: 8.97E-06;
mr1241_2 (Ind_All); LR P-value: 6.35E-09;
mr1246_2 (All); LR P-value: 1.08E-77;
mr1246_2 (Ind_All); LR P-value: 9.68E-08;
mr1264_2 (All); LR P-value: 8.65E-39;
mr1264_2 (Ind_All); LR P-value: 3.87E-08;
mr1270_2 (All); LR P-value: 6.17E-28;
mr1404_2 (Ind_All); LR P-value: 1.11E-06;
mr1437_2 (Ind_All); LR P-value: 4.31E-12;
mr1514_2 (All); LR P-value: 1.33E-12;
mr1620_2 (Ind_All); LR P-value: 1.46E-07;
mr1623_2 (All); LR P-value: 4.41E-07;
mr1690_2 (All); LR P-value: 4.85E-08;
mr1734_2 (All); LR P-value: 1.28E-11;
mr1744_2 (All); LR P-value: 1.68E-16;
mr1782_2 (All); LR P-value: 7.62E-11;
mr1878_2 (Ind_All); LR P-value: 1.07E-07;
mr1949_2 (Ind_All); LR P-value: 5.31E-08
LOC_Os12g04130.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 71.888; most accessible tissue: Zhenshan97 panicle, score: 90.061
vg1201734967 (J) chr12 1734967 T C 44.40% 6.07% T -> C NA
LOC_Os12g04130.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os12g04130.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 58.641; most accessible tissue: Callus, score: 97.001
vg1201734981 (J) chr12 1734981 G GACACAG CC 44.60% 5.12% GACACAGCC -> G NA
LOC_Os12g04130.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g04130.1 Alt: G| frameshift_variant&stop_lost&splice_region_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os12g04130.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 54.470; most accessible tissue: Callus, score: 97.001