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Search Results:

22 variations found. Os01g0872500/LOC_Os01g65200 (proton-dependent oligopeptide transport; putative; expressed), ranging from 37,834,176 bp to 37,836,926 bp (including 0 kb upstream and 0 kb downstream of the gene).

Gene IDAnnotation
LOC_Os01g65200 proton-dependent oligopeptide transport, putative, expressed; RAP ID: Os01g0872500; MSU ID: LOC_Os01g65200

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
vg0137834227 (J) chr01 37834227 C T 77.20% 0.00% C -> T
mr1375 (Ind_All); LR P-value: 4.54E-07;
mr1517 (All); LMM P-value: 1.34E-08;
mr1517 (Ind_All); LMM P-value: 3.59E-14; LR P-value: 2.14E-16;
mr1538 (All); LMM P-value: 4.03E-08;
mr1538 (Ind_All); LMM P-value: 4.97E-11; LR P-value: 2.53E-13;
mr1517_2 (All); LMM P-value: 7.43E-10;
mr1517_2 (Ind_All); LMM P-value: 6.44E-17; LR P-value: 3.14E-17;
mr1538_2 (All); LMM P-value: 9.55E-09;
mr1538_2 (Ind_All); LMM P-value: 9.97E-13; LR P-value: 5.59E-18
LOC_Os01g65200.3 Alt: T| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.1 Alt: T| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.2 Alt: T| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.3 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65210.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65190.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 87.421; most accessible tissue: Zhenshan97 panicle, score: 94.440
vg0137834291 (J) chr01 37834291 TCGGCCG TC T 57.60% 2.24% TCGGCCGTC -> T NA
LOC_Os01g65200.3 Alt: T| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os01g65200.1 Alt: T| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os01g65200.2 Alt: T| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os01g65200.3 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g65200.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g65200.2 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 89.315; most accessible tissue: Zhenshan97 panicle, score: 96.214
vg0137834297 (J) chr01 37834297 G T 86.90% 3.20% G -> T NA
LOC_Os01g65200.3 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g65200.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g65200.2 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g65200.3 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g65200.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g65200.2 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 89.326; most accessible tissue: Zhenshan97 panicle, score: 96.173
vg0137834298 (J) chr01 37834298 T C 86.90% 3.20% T -> C NA
LOC_Os01g65200.3 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g65200.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g65200.2 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g65200.3 Alt: C| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g65200.1 Alt: C| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g65200.2 Alt: C| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 89.326; most accessible tissue: Zhenshan97 panicle, score: 96.173
vg0137834337 (J) chr01 37834337 C T 82.60% 0.00% C -> T
mr1375 (Ind_All); LR P-value: 1.18E-06;
mr1517 (All); LMM P-value: 8.29E-10;
mr1517 (Ind_All); LMM P-value: 4.44E-14; LR P-value: 3.13E-16;
mr1538 (All); LMM P-value: 2.06E-08;
mr1538 (Ind_All); LMM P-value: 8.43E-11; LR P-value: 4.13E-13;
mr1517_2 (All); LMM P-value: 7.00E-10;
mr1517_2 (Ind_All); LMM P-value: 3.71E-16; LR P-value: 1.21E-16;
mr1538_2 (All); LMM P-value: 9.30E-08;
mr1538_2 (Ind_All); LMM P-value: 2.11E-11; LR P-value: 7.57E-17
LOC_Os01g65200.3 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g65200.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g65200.2 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 87.075; most accessible tissue: Zhenshan97 panicle, score: 96.335
vg0137834366 (J) chr01 37834366 T TC 94.80% 0.00% T -> TC NA
LOC_Os01g65210.1 Alt: TC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65190.1 Alt: TC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.3 Alt: TC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.1 Alt: TC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.2 Alt: TC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 87.654; most accessible tissue: Zhenshan97 panicle, score: 96.414
vg0137834378 (J) chr01 37834378 A G 82.40% 0.00% A -> G
mr1375 (Ind_All); LR P-value: 8.44E-07;
mr1517 (All); LMM P-value: 6.14E-10;
mr1517 (Ind_All); LMM P-value: 4.86E-14; LR P-value: 3.50E-16;
mr1538 (All); LMM P-value: 1.00E-08;
mr1538 (Ind_All); LMM P-value: 5.07E-11; LR P-value: 2.19E-13;
mr1517_2 (All); LMM P-value: 7.12E-10;
mr1517_2 (Ind_All); LMM P-value: 9.28E-16; LR P-value: 3.84E-16;
mr1538_2 (All); LMM P-value: 3.12E-08;
mr1538_2 (Ind_All); LMM P-value: 9.61E-12; LR P-value: 6.25E-17
LOC_Os01g65210.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65190.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.3 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 88.250; most accessible tissue: Zhenshan97 panicle, score: 96.863
vg0137834382 (J) chr01 37834382 G GGGC 60.10% 0.00% GGGC -> G NA
LOC_Os01g65210.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65190.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.3 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 87.742; most accessible tissue: Zhenshan97 panicle, score: 96.832
vg0137834439 (J) chr01 37834439 ACT ACTCT 63.30% 0.00% ACTCT -> ACT,A,ACTC TCT NA
LOC_Os01g65210.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os01g65190.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os01g65200.3 Alt: A| intron_variant MODIFIER(snpEff)
LOC_Os01g65200.1 Alt: A| intron_variant MODIFIER(snpEff)
LOC_Os01g65200.2 Alt: A| intron_variant MODIFIER(snpEff)
LOC_Os01g65210.1 Alt: ACTCTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65190.1 Alt: ACTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.3 Alt: ACTCTCT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.1 Alt: ACTCTCT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.2 Alt: ACTCTCT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65210.1 Alt: ACT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65190.1 Alt: ACT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.3 Alt: ACT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.1 Alt: ACT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.2 Alt: ACT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 89.728; most accessible tissue: Zhenshan97 panicle, score: 97.011
vg0137834644 (J) chr01 37834644 C T 97.80% 0.00% C -> T NA
LOC_Os01g65200.3 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os01g65200.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os01g65200.2 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 87.240; most accessible tissue: Zhenshan97 panicle, score: 95.855
vg0137834687 (J) chr01 37834687 C T 64.80% 0.00% T -> C NA
LOC_Os01g65200.3 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os01g65200.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os01g65200.2 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 86.515; most accessible tissue: Zhenshan97 panicle, score: 94.026
vg0137835203 (J) chr01 37835203 T G 58.20% 0.32% T -> G
mr1375 (All); LMM P-value: 2.16E-08; LR P-value: 1.31E-25;
mr1375 (Ind_All); LR P-value: 7.85E-08;
mr1517 (All); LMM P-value: 4.72E-19;
mr1517 (Ind_All); LMM P-value: 3.70E-15; LR P-value: 1.39E-18;
mr1538 (All); LMM P-value: 3.11E-17; LR P-value: 2.39E-72;
mr1538 (Ind_All); LMM P-value: 2.36E-10; LR P-value: 5.42E-13;
mr1517_2 (All); LMM P-value: 1.17E-25;
mr1517_2 (Ind_All); LMM P-value: 3.28E-20; LR P-value: 2.21E-21;
mr1538_2 (All); LMM P-value: 1.78E-19;
mr1538_2 (Ind_All); LMM P-value: 2.24E-12; LR P-value: 1.95E-18
LOC_Os01g65200.3 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g65200.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g65200.2 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g65200.3 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g65200.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g65200.2 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 60.720; most accessible tissue: Zhenshan97 young leaf, score: 80.056
vg0137835951 (J) chr01 37835951 G C 64.80% 0.00% C -> G NA
LOC_Os01g65200.3 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 68.825; most accessible tissue: Callus, score: 83.050
vg0137836018 (J) chr01 37836018 C T 57.80% 0.34% C -> T
mr1170 (All); LR P-value: 4.12E-12;
mr1375 (All); LMM P-value: 4.15E-10; LR P-value: 2.36E-27;
mr1375 (Ind_All); LMM P-value: 8.77E-07; LR P-value: 6.45E-09;
mr1517 (All); LMM P-value: 1.25E-19;
mr1517 (Ind_All); LMM P-value: 4.39E-15; LR P-value: 6.66E-19;
mr1538 (All); LMM P-value: 2.70E-19; LR P-value: 1.62E-73;
mr1538 (Ind_All); LMM P-value: 5.38E-11; LR P-value: 6.57E-14;
mr1517_2 (All); LMM P-value: 2.96E-29;
mr1517_2 (Ind_All); LMM P-value: 1.38E-20; LR P-value: 1.09E-22;
mr1538_2 (All); LMM P-value: 7.74E-24;
mr1538_2 (Ind_All); LMM P-value: 2.78E-14; LR P-value: 4.07E-21
LOC_Os01g65200.3 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os01g65200.3 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 71.392; most accessible tissue: Minghui63 flower, score: 83.376
vg0137836095 (J) chr01 37836095 AT A 99.90% 0.00% AT -> A NA
LOC_Os01g65200.3 Alt: A| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os01g65200.1 Alt: A| frameshift_variant&stop_lost HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 73.095; most accessible tissue: Minghui63 flower, score: 87.747
vg0137836126 (J) chr01 37836126 G T 64.80% 0.02% T -> G NA
LOC_Os01g65200.3 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g65200.3 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 74.658; most accessible tissue: Minghui63 flower, score: 89.903
vg0137836312 (J) chr01 37836312 C T 77.00% 0.32% C -> T
mr1375 (Ind_All); LR P-value: 2.82E-07;
mr1517 (All); LMM P-value: 1.21E-08;
mr1517 (Ind_All); LMM P-value: 7.10E-14; LR P-value: 3.53E-16;
mr1538 (All); LMM P-value: 9.38E-08;
mr1538 (Ind_All); LMM P-value: 1.77E-10; LR P-value: 7.60E-13;
mr1517_2 (All); LMM P-value: 2.58E-10;
mr1517_2 (Ind_All); LMM P-value: 2.31E-17; LR P-value: 1.80E-17;
mr1538_2 (All); LMM P-value: 7.02E-08;
mr1538_2 (Ind_All); LMM P-value: 2.47E-12; LR P-value: 9.24E-18
LOC_Os01g65200.3 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os01g65200.3 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 78.272; most accessible tissue: Minghui63 flower, score: 92.115
vg0137836398 (J) chr01 37836398 G A 58.20% 0.30% G -> A
mr1170 (All); LR P-value: 2.66E-12;
mr1375 (All); LMM P-value: 7.00E-09; LR P-value: 1.93E-26;
mr1375 (Ind_All); LMM P-value: 1.93E-06; LR P-value: 1.16E-08;
mr1517 (All); LMM P-value: 1.79E-19;
mr1517 (Ind_All); LMM P-value: 1.27E-15; LR P-value: 2.93E-19;
mr1538 (All); LMM P-value: 7.75E-18; LR P-value: 1.14E-73;
mr1538 (Ind_All); LMM P-value: 4.08E-11; LR P-value: 4.43E-14;
mr1517_2 (All); LMM P-value: 3.85E-25;
mr1517_2 (Ind_All); LMM P-value: 1.21E-19; LR P-value: 4.60E-22;
mr1538_2 (All); LMM P-value: 5.06E-20;
mr1538_2 (Ind_All); LMM P-value: 3.20E-13; LR P-value: 3.35E-20
LOC_Os01g65200.3 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g65200.3 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 78.039; most accessible tissue: Minghui63 flower, score: 93.866
vg0137836480 (J) chr01 37836480 C T 77.00% 0.00% C -> T
mr1375 (Ind_All); LR P-value: 8.44E-07;
mr1517 (All); LMM P-value: 1.06E-08;
mr1517 (Ind_All); LMM P-value: 4.82E-14; LR P-value: 2.81E-16;
mr1538 (All); LMM P-value: 7.29E-08;
mr1538 (Ind_All); LMM P-value: 9.98E-11; LR P-value: 5.79E-13;
mr1517_2 (All); LMM P-value: 3.38E-10;
mr1517_2 (Ind_All); LMM P-value: 4.19E-17; LR P-value: 1.30E-17;
mr1538_2 (All); LMM P-value: 8.97E-08;
mr1538_2 (Ind_All); LMM P-value: 3.87E-12; LR P-value: 1.22E-17
LOC_Os01g65200.3 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 82.193; most accessible tissue: Minghui63 flower, score: 94.828
vg0137836599 (J) chr01 37836599 T C 64.80% 0.00% C -> T NA
LOC_Os01g65200.3 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65210.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65190.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 86.634; most accessible tissue: Minghui63 flower, score: 95.882
vg0137836689 (J) chr01 37836689 G A 58.20% 0.30% G -> A
mr1170 (All); LR P-value: 1.12E-12;
mr1375 (All); LMM P-value: 5.97E-09; LR P-value: 2.74E-26;
mr1375 (Ind_All); LMM P-value: 2.98E-06; LR P-value: 2.27E-08;
mr1517 (All); LMM P-value: 1.74E-19;
mr1517 (Ind_All); LMM P-value: 6.19E-16; LR P-value: 1.61E-19;
mr1538 (All); LMM P-value: 4.60E-18; LR P-value: 7.98E-74;
mr1538 (Ind_All); LMM P-value: 2.30E-11; LR P-value: 5.13E-14;
mr1517_2 (All); LMM P-value: 2.10E-26;
mr1517_2 (Ind_All); LMM P-value: 3.35E-21; LR P-value: 4.78E-23;
mr1538_2 (All); LMM P-value: 4.84E-21;
mr1538_2 (Ind_All); LMM P-value: 2.92E-14; LR P-value: 9.47E-21
LOC_Os01g65200.3 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65200.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65210.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65190.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 86.404; most accessible tissue: Minghui63 flower, score: 95.674
STR0137834367 (J) chr01 37834367 C CC 93.80% 0.00% C -> CC NA