21 variations found. LOC_Os06g08500 (BHLH transcription factor; putative; expressed), ranging from 4,192,206 bp to 4,194,416 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0604192312 (J) | chr06 | 4192312 | C | T | 99.40% | 0.00% | C -> T | NA |
LOC_Os06g08500.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os06g08490.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 81.868; most accessible tissue: Zhenshan97 root, score: 87.187 |
| vg0604192359 (J) | chr06 | 4192359 | C | T | 97.90% | 0.00% | C -> T | NA |
LOC_Os06g08500.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 80.631; most accessible tissue: Zhenshan97 panicle, score: 88.350 |
| vg0604192363 (J) | chr06 | 4192363 | C | T | 76.50% | 0.00% | T -> C |
mr1050 (Jap_All); LR P-value: 8.76E-06;
mr1115 (All); LMM P-value: 2.83E-11; LR P-value: 1.92E-30; mr1115 (Jap_All); LMM P-value: 1.85E-08; LR P-value: 1.22E-23; mr1137 (All); LR P-value: 1.13E-29; mr1241 (All); LMM P-value: 4.53E-07; LR P-value: 5.29E-60; mr1241 (Jap_All); LR P-value: 5.18E-12; mr1611 (All); LMM P-value: 5.19E-08; LR P-value: 4.35E-28; mr1611 (Jap_All); LR P-value: 1.68E-16; mr1629 (Jap_All); LR P-value: 2.25E-06; mr1920 (All); LMM P-value: 5.16E-11; LR P-value: 2.77E-30; mr1920 (Jap_All); LMM P-value: 1.09E-06; LR P-value: 5.83E-16; mr1115_2 (All); LMM P-value: 2.95E-08; LR P-value: 5.42E-31; mr1115_2 (Jap_All); LR P-value: 6.93E-19; mr1241_2 (All); LMM P-value: 8.39E-10; LR P-value: 2.28E-74; mr1241_2 (Jap_All); LR P-value: 1.79E-15; mr1363_2 (Jap_All); LR P-value: 4.36E-06; mr1611_2 (All); LR P-value: 1.29E-26; mr1611_2 (Jap_All); LR P-value: 2.52E-13; mr1629_2 (Jap_All); LR P-value: 2.55E-07; mr1793_2 (Jap_All); LR P-value: 5.04E-06 |
LOC_Os06g08500.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 80.105; most accessible tissue: Zhenshan97 panicle, score: 88.062 |
| vg0604192525 (J) | chr06 | 4192525 | TCCG | GCCG | 83.70% | 0.00% | TCCG -> T,GCCG,TCC GCCG |
mr1283 (All); LR P-value: 4.21E-06;
mr1314 (All); LR P-value: 6.60E-06; mr1417 (All); LR P-value: 2.58E-06; mr1424 (All); LR P-value: 1.15E-06; mr1485 (All); LR P-value: 6.33E-07; mr1512 (All); LR P-value: 4.70E-06; mr1611 (Ind_All); LR P-value: 2.69E-06; mr1634 (All); LR P-value: 4.35E-06; mr1665 (All); LR P-value: 5.85E-06; mr1759 (All); LR P-value: 4.05E-06; mr1774 (All); LR P-value: 2.16E-06; mr1787 (All); LR P-value: 4.26E-06; mr1820 (All); LR P-value: 5.04E-06; mr1906 (All); LR P-value: 6.96E-07; mr1909 (All); LR P-value: 1.38E-13; mr1920 (Ind_All); LR P-value: 2.64E-07; mr1921 (All); LR P-value: 4.99E-11; mr1939 (All); LR P-value: 9.52E-11; mr1952 (All); LR P-value: 5.49E-06 |
LOC_Os06g08500.1 Alt: TCCGCCG| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os06g08500.1 Alt: T| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar) LOC_Os06g08500.1 Alt: GCCG| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 79.896; most accessible tissue: Zhenshan97 young leaf, score: 88.878 |
| vg0604192528 (J) | chr06 | 4192528 | G | T | 84.00% | 0.00% | G -> T |
mr1050 (All); LR P-value: 5.88E-11;
mr1115 (All); LMM P-value: 3.27E-11; mr1115 (Jap_All); LMM P-value: 1.27E-07; LR P-value: 3.32E-22; mr1141 (Ind_All); LR P-value: 5.71E-17; mr1241 (Jap_All); LR P-value: 4.36E-12; mr1611 (Jap_All); LR P-value: 1.58E-15; mr1629 (Jap_All); LR P-value: 2.71E-06; mr1676 (Jap_All); LR P-value: 2.11E-06; mr1887 (All); LR P-value: 1.49E-06; mr1903 (Ind_All); LR P-value: 4.66E-09; mr1920 (All); LMM P-value: 8.56E-06; mr1920 (Jap_All); LMM P-value: 7.85E-06; LR P-value: 8.78E-15; mr1115_2 (All); LMM P-value: 1.98E-06; mr1115_2 (Jap_All); LR P-value: 6.76E-18; mr1141_2 (Ind_All); LR P-value: 2.55E-17; mr1241_2 (Jap_All); LR P-value: 1.07E-15; mr1347_2 (All); LR P-value: 8.64E-09; mr1611_2 (Jap_All); LR P-value: 1.98E-12; mr1629_2 (Jap_All); LR P-value: 2.13E-07; mr1769_2 (All); LR P-value: 1.79E-10; mr1793_2 (Jap_All); LR P-value: 5.30E-06; mr1889_2 (Ind_All); LR P-value: 2.38E-08; mr1907_2 (Ind_All); LR P-value: 6.77E-09; mr1934_2 (Ind_All); LR P-value: 1.72E-10 |
LOC_Os06g08500.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 79.952; most accessible tissue: Zhenshan97 young leaf, score: 88.878 |
| vg0604192581 (J) | chr06 | 4192581 | T | C | 76.40% | 0.00% | C -> T |
mr1050 (Jap_All); LR P-value: 8.76E-06;
mr1115 (All); LMM P-value: 1.45E-11; LR P-value: 1.62E-30; mr1115 (Jap_All); LMM P-value: 1.85E-08; LR P-value: 1.22E-23; mr1241 (All); LMM P-value: 4.14E-07; LR P-value: 2.51E-59; mr1241 (Jap_All); LR P-value: 5.18E-12; mr1611 (All); LMM P-value: 1.28E-07; LR P-value: 1.48E-27; mr1611 (Jap_All); LR P-value: 1.68E-16; mr1629 (Jap_All); LR P-value: 2.25E-06; mr1920 (All); LMM P-value: 6.01E-11; LR P-value: 3.29E-30; mr1920 (Jap_All); LMM P-value: 1.09E-06; LR P-value: 5.83E-16; mr1115_2 (All); LMM P-value: 1.09E-07; LR P-value: 6.79E-31; mr1115_2 (Jap_All); LR P-value: 6.93E-19; mr1241_2 (All); LMM P-value: 6.31E-09; LR P-value: 2.39E-72; mr1241_2 (Jap_All); LR P-value: 1.79E-15; mr1363_2 (Jap_All); LR P-value: 4.36E-06; mr1611_2 (All); LR P-value: 1.99E-26; mr1611_2 (Jap_All); LR P-value: 2.52E-13; mr1629_2 (Jap_All); LR P-value: 2.55E-07; mr1793_2 (Jap_All); LR P-value: 5.04E-06 |
LOC_Os06g08500.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 76.627; most accessible tissue: Zhenshan97 young leaf, score: 87.859 |
| vg0604192641 (J) | chr06 | 4192641 | G | A | 76.50% | 0.00% | A -> G |
mr1050 (Jap_All); LR P-value: 8.76E-06;
mr1115 (All); LMM P-value: 1.86E-12; LR P-value: 3.51E-31; mr1115 (Jap_All); LMM P-value: 1.85E-08; LR P-value: 1.22E-23; mr1137 (All); LR P-value: 2.36E-29; mr1241 (All); LMM P-value: 1.19E-08; LR P-value: 8.55E-62; mr1241 (Jap_All); LR P-value: 5.18E-12; mr1611 (All); LMM P-value: 1.49E-09; LR P-value: 2.95E-29; mr1611 (Jap_All); LR P-value: 1.68E-16; mr1629 (Jap_All); LR P-value: 2.25E-06; mr1789 (All); LR P-value: 5.75E-29; mr1844 (All); LR P-value: 9.74E-13; mr1879 (All); LR P-value: 1.21E-11; mr1920 (All); LMM P-value: 9.39E-12; LR P-value: 9.36E-31; mr1920 (Jap_All); LMM P-value: 1.09E-06; LR P-value: 5.83E-16; mr1115_2 (All); LMM P-value: 3.13E-08; LR P-value: 7.77E-31; mr1115_2 (Jap_All); LR P-value: 6.93E-19; mr1241_2 (All); LMM P-value: 8.43E-10; LR P-value: 1.45E-73; mr1241_2 (Jap_All); LR P-value: 1.79E-15; mr1363_2 (Jap_All); LR P-value: 4.36E-06; mr1611_2 (All); LR P-value: 4.40E-26; mr1611_2 (Jap_All); LR P-value: 2.52E-13; mr1629_2 (Jap_All); LR P-value: 2.55E-07; mr1789_2 (All); LR P-value: 2.21E-28; mr1793_2 (Jap_All); LR P-value: 5.04E-06 |
LOC_Os06g08490.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g08500.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 72.805; most accessible tissue: Zhenshan97 young leaf, score: 85.001 |
| vg0604192753 (J) | chr06 | 4192753 | C | G | 99.80% | 0.00% | C -> G | NA |
LOC_Os06g08500.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 67.583; most accessible tissue: Zhenshan97 young leaf, score: 78.347 |
| vg0604192830 (J) | chr06 | 4192830 | T | C | 91.20% | 0.00% | T -> C | NA |
LOC_Os06g08490.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g08500.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 56.605; most accessible tissue: Zhenshan97 young leaf, score: 71.497 |
| vg0604193077 (J) | chr06 | 4193077 | T | G | 76.30% | 0.00% | G -> T |
mr1050 (Jap_All); LR P-value: 8.76E-06;
mr1115 (All); LMM P-value: 3.14E-11; LR P-value: 4.67E-30; mr1115 (Jap_All); LMM P-value: 1.85E-08; LR P-value: 1.22E-23; mr1137 (All); LR P-value: 1.56E-29; mr1241 (All); LMM P-value: 3.53E-07; LR P-value: 6.43E-60; mr1241 (Jap_All); LR P-value: 5.18E-12; mr1611 (All); LMM P-value: 1.69E-07; LR P-value: 3.65E-27; mr1611 (Jap_All); LR P-value: 1.68E-16; mr1629 (Jap_All); LR P-value: 2.25E-06; mr1920 (All); LMM P-value: 1.87E-10; LR P-value: 2.02E-29; mr1920 (Jap_All); LMM P-value: 1.09E-06; LR P-value: 5.83E-16; mr1115_2 (All); LMM P-value: 5.34E-08; LR P-value: 6.96E-31; mr1115_2 (Jap_All); LR P-value: 6.93E-19; mr1241_2 (All); LMM P-value: 1.36E-09; LR P-value: 5.55E-74; mr1241_2 (Jap_All); LR P-value: 1.79E-15; mr1363_2 (Jap_All); LR P-value: 4.36E-06; mr1611_2 (All); LR P-value: 6.66E-26; mr1611_2 (Jap_All); LR P-value: 2.52E-13; mr1629_2 (Jap_All); LR P-value: 2.55E-07; mr1793_2 (Jap_All); LR P-value: 5.04E-06 |
LOC_Os06g08490.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g08500.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 44.101; most accessible tissue: Minghui63 root, score: 54.099 |
| vg0604193278 (J) | chr06 | 4193278 | C | CA | 56.60% | 0.00% | C -> CA | NA |
LOC_Os06g08490.1 Alt: CA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g08500.1 Alt: CA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 39.659; most accessible tissue: Callus, score: 67.489 |
| vg0604193282 (J) | chr06 | 4193282 | A | G | 99.90% | 0.00% | A -> G | NA |
LOC_Os06g08490.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os06g08500.1 Alt: G| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 39.659; most accessible tissue: Callus, score: 67.489 |
| vg0604193490 (J) | chr06 | 4193490 | T | C | 99.90% | 0.00% | T -> C | NA |
LOC_Os06g08490.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
LOC_Os06g08500.1 Alt: C| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 56.364; most accessible tissue: Callus, score: 79.267 |
| vg0604193508 (J) | chr06 | 4193508 | CA | C | 56.60% | 0.00% | CA -> C | NA |
LOC_Os06g08490.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g08500.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 56.851; most accessible tissue: Callus, score: 79.267 |
| vg0604193650 (J) | chr06 | 4193650 | G | C | 99.90% | 0.00% | G -> C | NA |
LOC_Os06g08490.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
LOC_Os06g08500.1 Alt: C| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 64.776; most accessible tissue: Minghui63 panicle, score: 82.128 |
| vg0604193652 (J) | chr06 | 4193652 | C | G | 99.30% | 0.00% | C -> G | NA |
LOC_Os06g08490.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g08500.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 64.919; most accessible tissue: Minghui63 panicle, score: 82.128 |
| vg0604193682 (J) | chr06 | 4193682 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os06g08490.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os06g08500.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 67.544; most accessible tissue: Minghui63 panicle, score: 82.128 |
| vg0604193773 (J) | chr06 | 4193773 | A | T | 83.80% | 0.00% | A -> T |
mr1039 (Ind_All); LR P-value: 1.38E-07;
mr1050 (All); LR P-value: 1.90E-10; mr1115 (All); LMM P-value: 6.04E-10; mr1115 (Jap_All); LMM P-value: 1.27E-07; LR P-value: 3.32E-22; mr1141 (Ind_All); LR P-value: 3.56E-17; mr1241 (Jap_All); LR P-value: 4.36E-12; mr1593 (All); LR P-value: 1.62E-08; mr1611 (Jap_All); LR P-value: 1.58E-15; mr1629 (Jap_All); LR P-value: 2.71E-06; mr1676 (Jap_All); LR P-value: 2.11E-06; mr1887 (All); LR P-value: 4.14E-06; mr1920 (Jap_All); LMM P-value: 7.85E-06; LR P-value: 8.78E-15; mr1115_2 (All); LMM P-value: 4.32E-06; mr1115_2 (Jap_All); LR P-value: 6.76E-18; mr1141_2 (Ind_All); LR P-value: 1.57E-17; mr1241_2 (Jap_All); LR P-value: 1.07E-15; mr1347_2 (All); LR P-value: 1.22E-08; mr1611_2 (Jap_All); LR P-value: 1.98E-12; mr1629_2 (Jap_All); LR P-value: 2.13E-07; mr1769_2 (All); LR P-value: 3.51E-10; mr1793_2 (Jap_All); LR P-value: 5.30E-06; mr1934_2 (Ind_All); LR P-value: 3.68E-09 |
LOC_Os06g08490.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g08500.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 69.055; most accessible tissue: Minghui63 panicle, score: 83.421 |
| vg0604193908 (J) | chr06 | 4193908 | C | A | 76.50% | 0.00% | A -> C |
mr1115 (All); LMM P-value: 3.48E-10; LR P-value: 5.67E-29;
mr1115 (Jap_All); LMM P-value: 6.85E-07; LR P-value: 6.66E-21; mr1137 (All); LR P-value: 4.35E-29; mr1241 (All); LMM P-value: 1.53E-07; LR P-value: 1.20E-60; mr1241 (Jap_All); LR P-value: 5.53E-12; mr1611 (All); LMM P-value: 7.05E-08; LR P-value: 2.47E-27; mr1611 (Jap_All); LR P-value: 1.07E-15; mr1629 (Jap_All); LR P-value: 8.35E-07; mr1920 (All); LMM P-value: 3.16E-10; LR P-value: 6.03E-29; mr1920 (Jap_All); LMM P-value: 5.32E-06; LR P-value: 1.21E-14; mr1115_2 (All); LMM P-value: 5.34E-08; LR P-value: 1.74E-30; mr1115_2 (Jap_All); LR P-value: 9.28E-18; mr1241_2 (All); LMM P-value: 1.78E-09; LR P-value: 7.29E-74; mr1241_2 (Jap_All); LR P-value: 1.07E-14; mr1611_2 (All); LR P-value: 7.88E-26; mr1611_2 (Jap_All); LR P-value: 1.67E-12; mr1629_2 (Jap_All); LR P-value: 5.97E-08; mr1789_2 (All); LR P-value: 2.58E-28; mr1793_2 (Jap_All); LR P-value: 9.30E-06; mr1966_2 (Jap_All); LR P-value: 4.10E-06 |
LOC_Os06g08500.1 Alt: C| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os06g08490.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 65.318; most accessible tissue: Zhenshan97 root, score: 78.630 |
| vg0604193967 (J) | chr06 | 4193967 | C | A | 76.50% | 0.00% | A -> C |
mr1050 (Jap_All); LR P-value: 7.01E-06;
mr1115 (All); LMM P-value: 1.50E-12; LR P-value: 3.68E-31; mr1115 (Jap_All); LMM P-value: 6.34E-09; LR P-value: 3.00E-24; mr1137 (All); LR P-value: 1.02E-30; mr1241 (All); LMM P-value: 2.96E-08; LR P-value: 6.54E-62; mr1241 (Jap_All); LR P-value: 2.30E-12; mr1611 (All); LMM P-value: 2.81E-08; LR P-value: 5.07E-28; mr1611 (Jap_All); LR P-value: 1.03E-16; mr1629 (Jap_All); LR P-value: 2.48E-06; mr1920 (All); LMM P-value: 3.09E-11; LR P-value: 3.45E-30; mr1920 (Jap_All); LMM P-value: 8.22E-07; LR P-value: 3.86E-16; mr1115_2 (All); LMM P-value: 4.12E-10; LR P-value: 7.03E-33; mr1115_2 (Jap_All); LMM P-value: 3.84E-06; LR P-value: 6.64E-20; mr1137_2 (All); LR P-value: 5.43E-32; mr1241_2 (All); LMM P-value: 1.70E-12; LR P-value: 2.27E-78; mr1241_2 (Jap_All); LR P-value: 2.20E-16; mr1363_2 (Jap_All); LR P-value: 2.92E-06; mr1611_2 (All); LMM P-value: 1.05E-06; LR P-value: 6.75E-28; mr1611_2 (Jap_All); LR P-value: 4.69E-14; mr1629_2 (Jap_All); LR P-value: 1.50E-07; mr1789_2 (All); LR P-value: 1.59E-29; mr1793_2 (Jap_All); LR P-value: 5.22E-06 |
LOC_Os06g08490.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g08500.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 67.129; most accessible tissue: Zhenshan97 root, score: 75.661 |
| STR0604193279 (J) | chr06 | 4193279 | AA | AAA | 53.90% | 0.00% | AA -> AAA | NA |
|