24 variations found. 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).
| 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 |
|---|---|---|---|---|---|---|---|---|---|
| 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 |