30 variations found. LOC_Os06g41850 (SMP-30%2FGluconolaconase%2FLRE-like region containing protein; expressed), ranging from 25,093,241 bp to 25,094,294 bp (including 0 kb upstream and 0 kb downstream of the gene).
Rice quantitative trait nucleotides (QTNs) and inferred QTN effects are from Wei et al., Nature Genetics, 2021.
Category | Variant ID | Chrom | Pos | Gene | MSU | RAP | Alt_Allele_Function | Ref_geno | Alt_geno |
---|---|---|---|---|---|---|---|---|---|
Yield components | vg0625093552 | Chr6 | 25093552 | TGW6 | LOC_Os06g41850 | Os06g0623700 | increasing grain weight | CG | C |
Yield components | vg0625093498 | Chr6 | 25093498 | TGW6 | LOC_Os06g41850 | Os06g0623700 | increasing grain weight | CCGCT | C |
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 |
---|---|---|---|---|---|---|---|---|---|
vg0625093433 (J) | chr06 | 25093433 | C | T | 99.30% | 0.00% | C -> T | NA |
LOC_Os06g41850.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 86.184; most accessible tissue: Minghui63 panicle, score: 90.408 |
vg0625093499 (J) | chr06 | 25093499 | G | C | 90.90% | 0.00% | C -> G |
LOC_Os06g41850.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 85.648; most accessible tissue: Minghui63 panicle, score: 90.408 |
|
vg0625093552 (J) | chr06 | 25093552 | CG | C | 86.40% | 0.34% | CG -> C | NA |
LOC_Os06g41850.1 Alt: C| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os06g41850.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 84.621; most accessible tissue: Zhenshan97 root, score: 87.992 |
vg0625093574 (J) | chr06 | 25093574 | C | T | 99.60% | 0.00% | C -> T | NA |
LOC_Os06g41850.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 84.538; most accessible tissue: Minghui63 flower, score: 88.026 |
vg0625093577 (J) | chr06 | 25093577 | G | A | 99.60% | 0.00% | G -> A | NA |
LOC_Os06g41850.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 82.052; most accessible tissue: Minghui63 young leaf, score: 87.965 |
vg0625093598 (J) | chr06 | 25093598 | C | T | 99.60% | 0.00% | C -> T | NA |
LOC_Os06g41850.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 81.061; most accessible tissue: Minghui63 panicle, score: 87.605 |
vg0625093688 (J) | chr06 | 25093688 | G | T | 99.60% | 0.00% | G -> T | NA |
LOC_Os06g41850.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os06g41840.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os06g41860.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os06g41840.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os06g41840.3 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os06g41840.4 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 80.862; most accessible tissue: Minghui63 flower, score: 86.112 |
vg0625093697 (J) | chr06 | 25093697 | C | A | 99.60% | 0.00% | C -> A | NA |
LOC_Os06g41850.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 80.797; most accessible tissue: Minghui63 flower, score: 85.937 |
vg0625093708 (J) | chr06 | 25093708 | C | T | 91.10% | 0.00% | T -> C |
LOC_Os06g41850.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 80.662; most accessible tissue: Minghui63 flower, score: 85.848 |
|
vg0625093757 (J) | chr06 | 25093757 | T | C | 93.60% | 0.00% | T -> C |
mr1157 (All); LR P-value: 6.72E-07;
mr1446 (All); LR P-value: 4.58E-08; mr1652 (All); LR P-value: 4.54E-07; mr1855 (All); LR P-value: 1.06E-17; mr1123_2 (All); LR P-value: 3.21E-21; mr1317_2 (All); LR P-value: 3.04E-10; mr1610_2 (All); LR P-value: 1.80E-11; mr1855_2 (All); LR P-value: 1.87E-21; mr1897_2 (All); LR P-value: 1.48E-10; mr1914_2 (All); LR P-value: 1.41E-13; mr1927_2 (All); LR P-value: 2.74E-17 |
LOC_Os06g41850.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 79.450; most accessible tissue: Minghui63 flower, score: 84.058 |
vg0625093775 (J) | chr06 | 25093775 | T | G | 55.90% | 0.36% | T -> G | NA |
LOC_Os06g41850.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g41850.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 78.616; most accessible tissue: Minghui63 young leaf, score: 83.907 |
vg0625093784 (J) | chr06 | 25093784 | C | T | 99.60% | 0.00% | C -> T | NA |
LOC_Os06g41850.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 74.712; most accessible tissue: Zhenshan97 root, score: 80.680 |
vg0625093787 (J) | chr06 | 25093787 | T | C | 57.00% | 0.00% | C -> T |
mr1064 (All); LR P-value: 6.72E-38;
mr1151 (All); LR P-value: 3.11E-09; mr1249 (All); LR P-value: 5.03E-08; mr1534 (All); LR P-value: 3.89E-42; mr1697 (Ind_All); LMM P-value: 1.53E-07; mr1793 (All); LR P-value: 6.54E-29; mr1805 (Ind_All); LR P-value: 6.35E-06; mr1148_2 (All); LR P-value: 8.30E-15; mr1323_2 (All); LR P-value: 4.48E-26; mr1531_2 (All); LR P-value: 3.35E-20; mr1531_2 (Ind_All); LR P-value: 1.31E-06; mr1548_2 (All); LR P-value: 7.01E-07; mr1571_2 (All); LR P-value: 4.16E-34; mr1623_2 (All); LR P-value: 3.50E-07; mr1734_2 (All); LR P-value: 1.61E-10; mr1782_2 (All); LR P-value: 4.57E-10; mr1793_2 (All); LR P-value: 7.48E-45 |
LOC_Os06g41850.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 74.743; most accessible tissue: Zhenshan97 root, score: 80.680 |
vg0625093789 (J) | chr06 | 25093789 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os06g41850.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 74.142; most accessible tissue: Zhenshan97 root, score: 80.448 |
vg0625093892 (J) | chr06 | 25093892 | G | T | 57.00% | 0.00% | T -> G |
mr1064 (All); LR P-value: 4.16E-40;
mr1077 (All); LR P-value: 8.18E-19; mr1246 (All); LR P-value: 4.64E-61; mr1249 (All); LR P-value: 6.98E-08; mr1534 (All); LR P-value: 9.56E-45; mr1793 (All); LR P-value: 2.78E-28; mr1878 (All); LR P-value: 2.63E-32; mr1973 (All); LR P-value: 8.66E-82; mr1064_2 (All); LR P-value: 9.87E-60; mr1154_2 (All); LR P-value: 4.02E-51; mr1270_2 (All); LR P-value: 4.54E-27; mr1323_2 (All); LR P-value: 2.59E-27; mr1325_2 (All); LR P-value: 9.17E-13; mr1531_2 (All); LR P-value: 1.16E-19; mr1548_2 (All); LR P-value: 6.55E-07; mr1571_2 (All); LR P-value: 3.16E-34; mr1623_2 (All); LR P-value: 4.33E-07; mr1660_2 (All); LR P-value: 1.84E-08; mr1686_2 (All); LR P-value: 5.11E-15; mr1744_2 (All); LR P-value: 3.18E-16; mr1973_2 (All); LR P-value: 2.49E-95 |
LOC_Os06g41850.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 66.529; most accessible tissue: Minghui63 root, score: 77.009 |
vg0625093931 (J) | chr06 | 25093931 | T | G | 65.20% | 0.00% | G -> T |
mr1028 (All); LR P-value: 2.53E-06;
mr1190 (All); LR P-value: 5.43E-07; mr1245 (All); LR P-value: 9.40E-08; mr1256 (All); LR P-value: 1.38E-29; mr1276 (All); LR P-value: 5.64E-16; mr1369 (All); LR P-value: 1.02E-06; mr1439 (All); LR P-value: 4.50E-08; mr1442 (All); LR P-value: 8.00E-09; mr1453 (All); LR P-value: 5.88E-07; mr1690 (All); LR P-value: 1.94E-07; mr1764 (All); LR P-value: 7.28E-07; mr1886 (All); LR P-value: 6.80E-07; mr1979 (All); LR P-value: 3.56E-07; mr1124_2 (All); LR P-value: 5.61E-54 |
LOC_Os06g41850.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 67.047; most accessible tissue: Callus, score: 79.373 |
vg0625094032 (J) | chr06 | 25094032 | C | T | 84.70% | 0.00% | T -> C |
LOC_Os06g41850.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 68.502; most accessible tissue: Callus, score: 79.373 |
|
vg0625094057 (J) | chr06 | 25094057 | T | C | 98.90% | 0.00% | T -> C | NA |
LOC_Os06g41850.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 67.635; most accessible tissue: Callus, score: 79.373 |
vg0625094117 (J) | chr06 | 25094117 | T | C | 99.90% | 0.00% | T -> C | NA |
LOC_Os06g41850.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 63.324; most accessible tissue: Minghui63 root, score: 76.119 |
vg0625094123 (J) | chr06 | 25094123 | T | C | 99.60% | 0.00% | T -> C | NA |
LOC_Os06g41850.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 63.259; most accessible tissue: Minghui63 root, score: 76.119 |
vg0625094132 (J) | chr06 | 25094132 | T | C | 99.90% | 0.00% | T -> C | NA |
LOC_Os06g41850.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 63.053; most accessible tissue: Minghui63 root, score: 75.806 |
vg0625094134 (J) | chr06 | 25094134 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os06g41850.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 62.266; most accessible tissue: Minghui63 root, score: 75.485 |
vg0625094161 (J) | chr06 | 25094161 | C | G | 99.90% | 0.00% | C -> G | NA |
LOC_Os06g41850.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 61.520; most accessible tissue: Minghui63 root, score: 75.155 |
vg0625094168 (J) | chr06 | 25094168 | G | Unkown | 99.80% | 0.15% | G -> A | NA |
LOC_Os06g41850.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os06g41840.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os06g41860.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os06g41840.2 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os06g41840.3 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os06g41840.4 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 60.812; most accessible tissue: Minghui63 root, score: 74.812 |
vg0625094177 (J) | chr06 | 25094177 | T | G | 99.60% | 0.15% | T -> G | NA |
LOC_Os06g41850.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g41850.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 61.115; most accessible tissue: Callus, score: 82.890 |
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