21 variations found. LOC_Os09g37200 (transferase family protein; putative; expressed), ranging from 21,463,618 bp to 21,465,476 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 |
|---|---|---|---|---|---|---|---|---|---|
| Secondary metabolism | vg0921464008 | Chr9 | 21464008 | OsAT4c | LOC_Os09g37200 | Os09g0544000 | fewer N-feruloylputrescine | G | A |
| 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0921463998 (J) | chr09 | 21463998 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os09g37200.1 Alt: A| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 81.669; most accessible tissue: Minghui63 root, score: 92.533 |
| vg0921464008 (J) | chr09 | 21464008 | G | A | 80.30% | 0.00% | G -> A |
mr1003 (All); LMM P-value: 1.35E-07;
mr1003 (Ind_All); LMM P-value: 3.77E-07; LR P-value: 1.96E-07; mr1004 (All); LR P-value: 3.05E-08; mr1004 (Ind_All); LR P-value: 3.03E-07; mr1006 (All); LMM P-value: 1.76E-08; LR P-value: 3.73E-12; mr1006 (Ind_All); LMM P-value: 1.38E-07; LR P-value: 2.92E-12; mr1007 (All); LMM P-value: 1.28E-07; LR P-value: 1.09E-11; mr1007 (Ind_All); LMM P-value: 9.41E-07; LR P-value: 3.26E-11; mr1051 (All); LMM P-value: 1.05E-07; mr1051 (Ind_All); LMM P-value: 2.12E-07; LR P-value: 1.80E-08; mr1052 (All); LMM P-value: 1.83E-08; LR P-value: 1.56E-12; mr1052 (Ind_All); LMM P-value: 1.03E-07; LR P-value: 1.05E-12; mr1216 (All); LR P-value: 4.49E-06; mr1536 (All); LMM P-value: 1.37E-07; mr1536 (Ind_All); LMM P-value: 1.06E-07; LR P-value: 2.54E-10; mr1004_2 (All); LMM P-value: 5.16E-09; LR P-value: 4.50E-14; mr1004_2 (Ind_All); LMM P-value: 1.90E-07; LR P-value: 7.70E-10; mr1006_2 (All); LMM P-value: 4.02E-11; LR P-value: 2.90E-14; mr1006_2 (Ind_All); LMM P-value: 5.49E-10; LR P-value: 9.55E-15; mr1008_2 (Ind_All); LR P-value: 2.18E-06; mr1051_2 (All); LMM P-value: 1.72E-12; mr1051_2 (Ind_All); LMM P-value: 1.31E-11; LR P-value: 1.08E-12; mr1536_2 (All); LMM P-value: 2.86E-10; mr1536_2 (Ind_All); LMM P-value: 2.35E-09; LR P-value: 2.12E-12; mr1986_2 (Ind_All); LR P-value: 6.73E-07 |
LOC_Os09g37200.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 82.249; most accessible tissue: Zhenshan97 root, score: 92.789 |
| vg0921464024 (J) | chr09 | 21464024 | A | G | 80.20% | 0.00% | A -> G |
mr1003 (All); LMM P-value: 1.20E-07;
mr1003 (Ind_All); LMM P-value: 6.18E-07; LR P-value: 3.01E-07; mr1004 (All); LR P-value: 3.68E-08; mr1004 (Ind_All); LR P-value: 1.86E-07; mr1006 (All); LMM P-value: 1.37E-08; LR P-value: 2.17E-12; mr1006 (Ind_All); LMM P-value: 1.30E-07; LR P-value: 2.27E-12; mr1007 (All); LMM P-value: 1.33E-07; LR P-value: 5.35E-12; mr1007 (Ind_All); LMM P-value: 7.85E-07; LR P-value: 1.79E-11; mr1051 (All); LMM P-value: 1.19E-07; mr1051 (Ind_All); LMM P-value: 4.08E-07; LR P-value: 3.44E-08; mr1052 (All); LMM P-value: 1.19E-08; LR P-value: 7.69E-13; mr1052 (Ind_All); LMM P-value: 8.42E-08; LR P-value: 6.42E-13; mr1536 (All); LMM P-value: 1.27E-07; mr1536 (Ind_All); LMM P-value: 6.69E-08; LR P-value: 5.47E-11; mr1004_2 (All); LMM P-value: 6.41E-10; LR P-value: 3.46E-15; mr1004_2 (Ind_All); LMM P-value: 5.22E-08; LR P-value: 1.03E-10; mr1006_2 (All); LMM P-value: 1.67E-11; LR P-value: 4.69E-15; mr1006_2 (Ind_All); LMM P-value: 2.89E-10; LR P-value: 3.55E-15; mr1008_2 (Ind_All); LR P-value: 6.73E-07; mr1051_2 (All); LMM P-value: 1.95E-12; mr1051_2 (Ind_All); LMM P-value: 1.92E-11; LR P-value: 2.44E-12; mr1536_2 (All); LMM P-value: 6.18E-10; mr1536_2 (Ind_All); LMM P-value: 7.94E-10; LR P-value: 2.05E-13; mr1986_2 (All); LMM P-value: 4.72E-06; LR P-value: 5.96E-11; mr1986_2 (Ind_All); LMM P-value: 5.13E-06; LR P-value: 2.14E-07 |
LOC_Os09g37200.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 82.393; most accessible tissue: Minghui63 root, score: 92.905 |
| vg0921464212 (J) | chr09 | 21464212 | G | A | 97.70% | 0.40% | G -> A | NA |
LOC_Os09g37200.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g37200.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 78.948; most accessible tissue: Minghui63 root, score: 91.021 |
| vg0921464318 (J) | chr09 | 21464318 | G | A | 81.80% | 1.27% | A -> G | NA |
LOC_Os09g37200.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os09g37200.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 77.892; most accessible tissue: Minghui63 root, score: 91.062 |
| vg0921464573 (J) | chr09 | 21464573 | C | T | 97.90% | 0.25% | C -> T | NA |
LOC_Os09g37200.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g37200.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 79.505; most accessible tissue: Minghui63 root, score: 90.555 |
| vg0921464634 (J) | chr09 | 21464634 | T | G | 99.80% | 0.00% | T -> G | NA |
LOC_Os09g37200.1 Alt: G| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 77.710; most accessible tissue: Minghui63 root, score: 91.062 |
| vg0921464761 (J) | chr09 | 21464761 | G | A | 98.60% | 0.00% | G -> A | NA |
LOC_Os09g37200.1 Alt: A| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 80.954; most accessible tissue: Zhenshan97 root, score: 92.108 |
| vg0921464793 (J) | chr09 | 21464793 | G | T | 98.20% | 0.00% | G -> T | NA |
LOC_Os09g37200.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 79.375; most accessible tissue: Zhenshan97 root, score: 91.763 |
| vg0921465144 (J) | chr09 | 21465144 | C | CAGT | 86.10% | 0.00% | C -> CAGT,CACCG | NA |
LOC_Os09g37200.1 Alt: CACCG| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g37200.1 Alt: CAGT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 69.347; most accessible tissue: Zhenshan97 root, score: 93.720 |
| vg0921465189 (J) | chr09 | 21465189 | C | A | 61.70% | 0.00% | C -> A |
mr1003 (All); LMM P-value: 1.01E-06; LR P-value: 1.37E-24;
mr1003 (Ind_All); LMM P-value: 5.30E-07; LR P-value: 4.72E-07; mr1004 (Ind_All); LR P-value: 2.27E-07; mr1006 (All); LR P-value: 2.74E-07; mr1006 (Ind_All); LMM P-value: 8.43E-07; LR P-value: 1.09E-11; mr1007 (Ind_All); LMM P-value: 5.67E-06; LR P-value: 5.93E-11; mr1051 (All); LMM P-value: 2.22E-06; LR P-value: 8.39E-26; mr1051 (Ind_All); LMM P-value: 6.09E-07; LR P-value: 7.67E-08; mr1052 (All); LR P-value: 1.58E-07; mr1052 (Ind_All); LMM P-value: 8.68E-07; LR P-value: 4.16E-12; mr1536 (All); LMM P-value: 2.60E-06; mr1536 (Ind_All); LMM P-value: 7.99E-08; LR P-value: 6.03E-11; mr1004_2 (All); LMM P-value: 1.69E-07; mr1004_2 (Ind_All); LMM P-value: 1.96E-06; LR P-value: 4.73E-10; mr1006_2 (All); LMM P-value: 8.78E-10; LR P-value: 4.12E-07; mr1006_2 (Ind_All); LMM P-value: 1.27E-09; LR P-value: 6.40E-15; mr1008_2 (Ind_All); LR P-value: 7.81E-07; mr1051_2 (All); LMM P-value: 1.51E-12; LR P-value: 7.13E-36; mr1051_2 (Ind_All); LMM P-value: 9.38E-12; LR P-value: 3.17E-12; mr1536_2 (All); LMM P-value: 7.68E-09; mr1536_2 (Ind_All); LMM P-value: 6.43E-10; LR P-value: 9.54E-14; mr1986_2 (Ind_All); LR P-value: 1.90E-07 |
LOC_Os09g37200.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 68.420; most accessible tissue: Callus, score: 94.334 |
| vg0921465202 (J) | chr09 | 21465202 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os09g37200.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
The average chromatin accessibility score: 68.990; most accessible tissue: Callus, score: 94.334 |
| vg0921465212 (J) | chr09 | 21465212 | GATT | GATTATT | 97.40% | 0.00% | GATT -> GATTATT,G | NA |
LOC_Os09g37200.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os09g37200.1 Alt: GATTATT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 69.071; most accessible tissue: Callus, score: 94.334 |
| vg0921465231 (J) | chr09 | 21465231 | A | AT | 95.30% | 0.00% | A -> AT | NA |
The average chromatin accessibility score: 68.423; most accessible tissue: Callus, score: 94.334
|
| vg0921465233 (J) | chr09 | 21465233 | A | T | 80.60% | 0.00% | A -> T,ATTATTAT T,ATTATT,A TTATTATTAT T,ATT,ATTA TTATTATTAT T |
mr1003 (All); LMM P-value: 1.48E-07;
mr1003 (Ind_All); LMM P-value: 6.18E-07; LR P-value: 3.01E-07; mr1004 (All); LR P-value: 5.43E-08; mr1004 (Ind_All); LR P-value: 1.86E-07; mr1006 (All); LMM P-value: 1.43E-08; LR P-value: 3.41E-12; mr1006 (Ind_All); LMM P-value: 1.30E-07; LR P-value: 2.27E-12; mr1007 (All); LMM P-value: 1.06E-07; LR P-value: 6.49E-12; mr1007 (Ind_All); LMM P-value: 7.85E-07; LR P-value: 1.79E-11; mr1051 (All); LMM P-value: 1.59E-07; mr1051 (Ind_All); LMM P-value: 4.08E-07; LR P-value: 3.44E-08; mr1052 (All); LMM P-value: 1.33E-08; LR P-value: 1.26E-12; mr1052 (Ind_All); LMM P-value: 8.42E-08; LR P-value: 6.42E-13; mr1536 (All); LMM P-value: 1.98E-07; mr1536 (Ind_All); LMM P-value: 6.69E-08; LR P-value: 5.47E-11; mr1004_2 (All); LMM P-value: 9.88E-10; LR P-value: 5.72E-15; mr1004_2 (Ind_All); LMM P-value: 5.22E-08; LR P-value: 1.03E-10; mr1006_2 (All); LMM P-value: 1.65E-11; LR P-value: 4.55E-15; mr1006_2 (Ind_All); LMM P-value: 2.89E-10; LR P-value: 3.55E-15; mr1008_2 (Ind_All); LR P-value: 6.73E-07; mr1051_2 (All); LMM P-value: 1.98E-12; mr1051_2 (Ind_All); LMM P-value: 1.92E-11; LR P-value: 2.44E-12; mr1536_2 (All); LMM P-value: 8.99E-10; mr1536_2 (Ind_All); LMM P-value: 7.94E-10; LR P-value: 2.05E-13; mr1986_2 (All); LMM P-value: 8.23E-06; LR P-value: 1.25E-10; mr1986_2 (Ind_All); LMM P-value: 5.13E-06; LR P-value: 2.14E-07 |
LOC_Os09g37200.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g37200.1 Alt: ATT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g37200.1 Alt: ATTATTATTATTATT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g37200.1 Alt: ATTATTATT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g37200.1 Alt: ATTATTATTATT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g37200.1 Alt: ATTATT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.030; most accessible tissue: Callus, score: 94.334 |
| vg0921465248 (J) | chr09 | 21465248 | T | C | 80.40% | 0.04% | T -> C |
mr1003 (All); LMM P-value: 8.26E-09;
mr1003 (Ind_All); LMM P-value: 1.20E-07; LR P-value: 7.20E-08; mr1004 (All); LMM P-value: 7.75E-06; LR P-value: 9.94E-09; mr1004 (Ind_All); LR P-value: 4.88E-08; mr1006 (All); LMM P-value: 3.78E-09; LR P-value: 3.42E-13; mr1006 (Ind_All); LMM P-value: 5.55E-08; LR P-value: 7.00E-13; mr1007 (All); LMM P-value: 7.41E-08; LR P-value: 2.23E-12; mr1007 (Ind_All); LMM P-value: 4.96E-07; LR P-value: 8.21E-12; mr1051 (All); LMM P-value: 6.18E-09; mr1051 (Ind_All); LMM P-value: 5.64E-08; LR P-value: 6.26E-09; mr1052 (All); LMM P-value: 1.63E-09; LR P-value: 6.31E-14; mr1052 (Ind_All); LMM P-value: 1.76E-08; LR P-value: 9.97E-14; mr1536 (All); LMM P-value: 1.49E-07; mr1536 (Ind_All); LMM P-value: 7.43E-08; LR P-value: 4.41E-11; mr1004_2 (All); LMM P-value: 4.48E-09; LR P-value: 1.37E-14; mr1004_2 (Ind_All); LMM P-value: 4.30E-07; LR P-value: 5.73E-10; mr1006_2 (All); LMM P-value: 4.29E-11; LR P-value: 3.99E-15; mr1006_2 (Ind_All); LMM P-value: 1.08E-09; LR P-value: 9.07E-15; mr1008_2 (Ind_All); LR P-value: 4.59E-07; mr1051_2 (All); LMM P-value: 7.90E-12; mr1051_2 (Ind_All); LMM P-value: 2.50E-10; LR P-value: 8.26E-12; mr1536_2 (All); LMM P-value: 1.50E-09; mr1536_2 (Ind_All); LMM P-value: 1.21E-09; LR P-value: 1.72E-13; mr1986_2 (All); LMM P-value: 2.54E-07; LR P-value: 9.83E-13; mr1986_2 (Ind_All); LMM P-value: 1.08E-06; LR P-value: 5.83E-08 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g37200.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 67.993; most accessible tissue: Callus, score: 94.334 |
| vg0921465274 (J) | chr09 | 21465274 | ATTTGTG CG | A | 98.60% | 0.00% | ATTTGTGCG -> A | NA |
LOC_Os09g37200.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
The average chromatin accessibility score: 62.323; most accessible tissue: Callus, score: 94.334 |
| vg0921465305 (J) | chr09 | 21465305 | A | C | 58.20% | 0.00% | C -> A | NA |
LOC_Os09g37200.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 61.114; most accessible tissue: Callus, score: 94.334 |
| vg0921465374 (J) | chr09 | 21465374 | T | G | 98.60% | 0.00% | T -> G | NA |
LOC_Os09g37200.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)
The average chromatin accessibility score: 54.961; most accessible tissue: Zhenshan97 root, score: 90.023 |
| vg0921465397 (J) | chr09 | 21465397 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os09g37200.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
The average chromatin accessibility score: 54.201; most accessible tissue: Zhenshan97 root, score: 89.064 |
| vg0921465436 (J) | chr09 | 21465436 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os09g37200.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
The average chromatin accessibility score: 54.281; most accessible tissue: Callus, score: 91.589 |