Search for Variation by Gene:

Gene ID/Symbol/Name (e.g., LOC_Os01g08570 or hwh1 or Os01g0180900 or gly%ltransferase, note: wildcard character '%' is also acceptable.):
Upstream (kb, optional, must <= 10 kb) : Downstream (kb, optional, must <= 10 kb) :
Variations Type:

Optional: (The selected data will be displayed in the result page.)
 Show Gene Expression Atlas  Show Chromatin Accessibility Map
 Show Non-coding variation Scores

Search Results:

41 variations found. Os01g0946700/LOC_Os01g71830 (glycosyl hydrolases family 17; putative; expressed), ranging from 41,603,296 bp to 41,604,680 bp (including 0 kb upstream and 0 kb downstream of the gene).

MSU IDRAP IDSymbolNameExplanationRecommended Gene SymbolRecommended Gene Name
LOC_Os01g71830Os01g0946700OsGLN1endo-1,3-beta-glucanase 1AF337174.__

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
vg0141603329 (J) chr01 41603329 T C 86.50% 0.00% T -> C NA
LOC_Os01g71830.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71820.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71840.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 51.265; most accessible tissue: Zhenshan97 root, score: 95.351
vg0141603416 (J) chr01 41603416 C A 51.40% 0.13% A -> C
mr1705 (All); LR P-value: 5.79E-06;
mr1974 (Ind_All); LR P-value: 1.79E-07;
mr1553_2 (All); LR P-value: 7.70E-15;
mr1553_2 (Ind_All); LR P-value: 3.49E-06;
mr1574_2 (All); LR P-value: 2.86E-06;
mr1974_2 (All); LR P-value: 1.66E-06
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g71820.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71840.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71830.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 55.792; most accessible tissue: Zhenshan97 root, score: 94.212
vg0141603439 (J) chr01 41603439 G T 51.30% 0.08% T -> G
mr1705 (All); LR P-value: 5.58E-06;
mr1974 (Ind_All); LR P-value: 4.20E-06;
mr1553_2 (All); LR P-value: 1.85E-14;
mr1553_2 (Ind_All); LR P-value: 8.69E-06;
mr1574_2 (All); LR P-value: 6.15E-07;
mr1974_2 (All); LR P-value: 4.85E-06
LOC_Os01g71820.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71840.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71830.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 59.525; most accessible tissue: Zhenshan97 root, score: 94.056
vg0141603781 (J) chr01 41603781 C G 92.60% 0.00% C -> G NA
LOC_Os01g71830.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 74.136; most accessible tissue: Zhenshan97 root, score: 94.079
vg0141603783 (J) chr01 41603783 G GT 99.70% 0.00% G -> GT NA
The average chromatin accessibility score: 74.099; most accessible tissue: Zhenshan97 root, score: 94.033
vg0141603784 (J) chr01 41603784 G T 92.60% 0.00% G -> T NA
LOC_Os01g71830.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 74.184; most accessible tissue: Zhenshan97 root, score: 94.056
vg0141603785 (J) chr01 41603785 A G 92.60% 0.00% A -> G NA
LOC_Os01g71830.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 74.153; most accessible tissue: Zhenshan97 root, score: 94.056
vg0141603799 (J) chr01 41603799 G C 51.00% 0.13% C -> G
mr1236 (Ind_All); LR P-value: 1.80E-07;
mr1729 (Ind_All); LR P-value: 8.73E-06;
mr1985 (Ind_All); LMM P-value: 1.68E-06; LR P-value: 1.68E-06;
mr1236_2 (Ind_All); LR P-value: 5.31E-06;
mr1553_2 (All); LR P-value: 1.92E-12;
mr1749_2 (All); LR P-value: 2.17E-07;
mr1974_2 (All); LR P-value: 2.88E-08;
mr1974_2 (Ind_All); LR P-value: 2.28E-07
LOC_Os01g71830.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g71830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 74.438; most accessible tissue: Zhenshan97 root, score: 93.988
vg0141603810 (J) chr01 41603810 G A 92.80% 0.00% G -> A NA
LOC_Os01g71830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 74.815; most accessible tissue: Zhenshan97 root, score: 93.988
vg0141603815 (J) chr01 41603815 T A 92.80% 0.00% T -> A NA
LOC_Os01g71830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 74.621; most accessible tissue: Zhenshan97 root, score: 93.917
vg0141603890 (J) chr01 41603890 G T 58.50% 0.00% T -> G
Spikelet_length (Ind_All); LR P-value: 3.75E-07;
mr1236 (Ind_All); LR P-value: 8.86E-06;
mr1322 (All); LR P-value: 7.39E-10;
mr1705 (All); LR P-value: 7.10E-06;
mr1038_2 (Ind_All); LR P-value: 5.22E-07;
mr1553_2 (All); LR P-value: 6.94E-14;
mr1574_2 (All); LR P-value: 1.94E-06;
mr1749_2 (All); LR P-value: 3.60E-08;
mr1821_2 (All); LR P-value: 6.08E-08;
mr1974_2 (All); LR P-value: 1.73E-07;
mr1974_2 (Ind_All); LR P-value: 1.01E-06
LOC_Os01g71830.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 69.944; most accessible tissue: Zhenshan97 root, score: 94.629
vg0141603896 (J) chr01 41603896 A G 92.40% 0.00% A -> G NA
LOC_Os01g71830.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 69.238; most accessible tissue: Zhenshan97 root, score: 94.590
vg0141604003 (J) chr01 41604003 G C 51.10% 3.32% C -> G
Spikelet_length (Ind_All); LR P-value: 3.75E-07;
mr1236 (Ind_All); LR P-value: 8.86E-06;
mr1322 (All); LR P-value: 5.91E-10;
mr1532 (All); LR P-value: 8.21E-06;
mr1038_2 (Ind_All); LR P-value: 5.22E-07;
mr1553_2 (All); LR P-value: 6.49E-14;
mr1574_2 (All); LR P-value: 1.84E-06;
mr1749_2 (All); LR P-value: 3.19E-08;
mr1821_2 (All); LR P-value: 6.53E-08;
mr1974_2 (All); LR P-value: 1.04E-07;
mr1974_2 (Ind_All); LR P-value: 1.01E-06
LOC_Os01g71830.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g71830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 69.721; most accessible tissue: Zhenshan97 root, score: 95.242
vg0141604009 (J) chr01 41604009 G T 51.20% 2.71% T -> G
Spikelet_length (Ind_All); LR P-value: 3.75E-07;
mr1236 (Ind_All); LR P-value: 8.86E-06;
mr1322 (All); LR P-value: 7.39E-10;
mr1705 (All); LR P-value: 7.10E-06;
mr1038_2 (Ind_All); LR P-value: 5.22E-07;
mr1553_2 (All); LR P-value: 6.94E-14;
mr1574_2 (All); LR P-value: 1.94E-06;
mr1749_2 (All); LR P-value: 3.60E-08;
mr1821_2 (All); LR P-value: 6.08E-08;
mr1974_2 (All); LR P-value: 1.73E-07;
mr1974_2 (Ind_All); LR P-value: 1.01E-06
LOC_Os01g71830.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g71830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 69.464; most accessible tissue: Zhenshan97 root, score: 95.258
vg0141604021 (J) chr01 41604021 G T 55.50% 0.95% T -> G
Spikelet_length (Ind_All); LR P-value: 3.75E-07;
mr1236 (Ind_All); LR P-value: 8.86E-06;
mr1322 (All); LR P-value: 7.39E-10;
mr1705 (All); LR P-value: 7.10E-06;
mr1038_2 (Ind_All); LR P-value: 5.22E-07;
mr1553_2 (All); LR P-value: 6.94E-14;
mr1574_2 (All); LR P-value: 1.94E-06;
mr1749_2 (All); LR P-value: 3.60E-08;
mr1821_2 (All); LR P-value: 6.08E-08;
mr1974_2 (All); LR P-value: 1.73E-07;
mr1974_2 (Ind_All); LR P-value: 1.01E-06
LOC_Os01g71830.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g71830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 69.174; most accessible tissue: Zhenshan97 root, score: 95.258
vg0141604068 (J) chr01 41604068 T C 92.20% 0.00% T -> C NA
LOC_Os01g71830.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 68.405; most accessible tissue: Zhenshan97 root, score: 95.209
vg0141604122 (J) chr01 41604122 A G 99.40% 0.00% A -> G NA
LOC_Os01g71830.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os01g71840.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 65.745; most accessible tissue: Zhenshan97 root, score: 95.080
vg0141604189 (J) chr01 41604189 C G 94.70% 0.00% C -> G NA
LOC_Os01g71830.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 64.134; most accessible tissue: Zhenshan97 root, score: 95.242
vg0141604194 (J) chr01 41604194 G A 52.30% 0.25% G -> A NA
LOC_Os01g71830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g71830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 63.449; most accessible tissue: Zhenshan97 root, score: 95.226
vg0141604214 (J) chr01 41604214 T A 99.40% 0.00% T -> A NA
LOC_Os01g71830.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os01g71840.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 61.936; most accessible tissue: Zhenshan97 root, score: 95.080
vg0141604253 (J) chr01 41604253 G A 49.90% 0.00% G -> A
mr1090 (Ind_All); LR P-value: 1.90E-06;
mr1236 (Ind_All); LR P-value: 4.42E-07;
mr1729 (Ind_All); LR P-value: 9.59E-06;
mr1985 (Ind_All); LMM P-value: 7.54E-07; LR P-value: 7.54E-07;
mr1553_2 (All); LR P-value: 3.43E-12;
mr1974_2 (All); LR P-value: 1.02E-07;
mr1974_2 (Ind_All); LR P-value: 4.81E-07
LOC_Os01g71830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 58.920; most accessible tissue: Zhenshan97 root, score: 94.723
vg0141604340 (J) chr01 41604340 G A 87.70% 1.99% G -> A
mr1585 (All); LR P-value: 5.19E-10;
mr1242_2 (All); LMM P-value: 8.63E-06
LOC_Os01g71830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os01g71830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 60.107; most accessible tissue: Zhenshan97 root, score: 95.226
vg0141604372 (J) chr01 41604372 C T 57.80% 1.84% C -> T
Plant_height (All); LR P-value: 3.27E-22;
Plant_height (Ind_All); LR P-value: 1.82E-16;
mr1192 (All); LR P-value: 4.38E-06;
mr1574 (All); LR P-value: 4.25E-07;
mr1765 (All); LR P-value: 6.52E-16;
mr1265_2 (All); LR P-value: 7.39E-09;
mr1265_2 (Ind_All); LR P-value: 8.45E-06;
mr1268_2 (Ind_All); LR P-value: 8.06E-08;
mr1327_2 (All); LR P-value: 1.67E-10;
mr1327_2 (Ind_All); LR P-value: 1.15E-10;
mr1378_2 (All); LR P-value: 1.89E-12;
mr1378_2 (Ind_All); LR P-value: 7.87E-08;
mr1522_2 (All); LR P-value: 6.02E-06;
mr1528_2 (All); LR P-value: 4.60E-07;
mr1817_2 (All); LR P-value: 1.88E-18;
mr1860_2 (Ind_All); LR P-value: 2.36E-06;
mr1971_2 (Ind_All); LR P-value: 3.99E-07;
mr1977_2 (All); LR P-value: 5.20E-07
LOC_Os01g71830.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g71830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 58.893; most accessible tissue: Zhenshan97 root, score: 95.304
vg0141604376 (J) chr01 41604376 C G 90.00% 2.86% C -> G NA
LOC_Os01g71830.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g71830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 58.220; most accessible tissue: Zhenshan97 root, score: 95.209
vg0141604377 (J) chr01 41604377 A T 90.00% 2.88% A -> T NA
LOC_Os01g71830.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g71830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 58.319; most accessible tissue: Zhenshan97 root, score: 95.242
vg0141604379 (J) chr01 41604379 C A 90.10% 2.86% C -> A NA
LOC_Os01g71830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g71830.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 55.839; most accessible tissue: Zhenshan97 root, score: 94.941
vg0141604381 (J) chr01 41604381 G C 90.20% 1.71% G -> C NA
LOC_Os01g71830.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g71830.1 Alt: C| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 55.795; most accessible tissue: Zhenshan97 root, score: 94.941
vg0141604457 (J) chr01 41604457 A T 96.40% 0.00% A -> T NA
LOC_Os01g71830.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 56.922; most accessible tissue: Zhenshan97 root, score: 95.226
vg0141604459 (J) chr01 41604459 T C 96.40% 0.00% T -> C NA
LOC_Os01g71830.1 Alt: C| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 56.842; most accessible tissue: Zhenshan97 root, score: 95.226
vg0141604539 (J) chr01 41604539 G T 57.90% 0.00% T -> G
Spikelet_length (Ind_All); LR P-value: 4.10E-07;
mr1322 (All); LR P-value: 1.41E-09;
mr1705 (All); LR P-value: 5.03E-06;
mr1553_2 (All); LR P-value: 5.89E-14;
mr1574_2 (All); LR P-value: 2.41E-06;
mr1749_2 (All); LR P-value: 1.18E-07;
mr1821_2 (All); LR P-value: 1.81E-07;
mr1974_2 (All); LR P-value: 4.39E-07;
mr1974_2 (Ind_All); LR P-value: 3.47E-06
LOC_Os01g71830.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71840.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 50.448; most accessible tissue: Zhenshan97 root, score: 94.667
vg0141604594 (J) chr01 41604594 A G 57.90% 0.00% G -> A
Spikelet_length (Ind_All); LR P-value: 6.04E-07;
mr1322 (All); LR P-value: 5.76E-10;
mr1705 (All); LR P-value: 4.33E-06;
mr1553_2 (All); LR P-value: 5.66E-14;
mr1574_2 (All); LR P-value: 2.24E-06;
mr1749_2 (All); LR P-value: 1.07E-07;
mr1821_2 (All); LR P-value: 1.84E-07;
mr1974_2 (All); LR P-value: 7.84E-07;
mr1974_2 (Ind_All); LR P-value: 7.85E-06
LOC_Os01g71830.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71840.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 46.484; most accessible tissue: Zhenshan97 root, score: 93.745
vg0141604600 (J) chr01 41604600 C T 84.80% 0.00% C -> T NA
LOC_Os01g71830.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71840.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 46.347; most accessible tissue: Zhenshan97 root, score: 93.695
vg0141604644 (J) chr01 41604644 G T 56.30% 0.06% T -> G NA
LOC_Os01g71830.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71840.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 43.129; most accessible tissue: Zhenshan97 root, score: 92.883
vg0141604645 (J) chr01 41604645 T A 55.50% 0.15% A -> T NA
LOC_Os01g71830.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71840.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 43.124; most accessible tissue: Zhenshan97 root, score: 92.820
vg0141604651 (J) chr01 41604651 TTACAA TAA 43.30% 25.77% TTACAA -> TAA,T NA
LOC_Os01g71830.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71840.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g71830.1 Alt: TAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71840.1 Alt: TAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 42.881; most accessible tissue: Zhenshan97 root, score: 92.627
vg0141604652 (J) chr01 41604652 T A 47.90% 11.17% T -> A NA
LOC_Os01g71830.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71840.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 42.881; most accessible tissue: Zhenshan97 root, score: 92.627
vg0141604654 (J) chr01 41604654 C A 48.10% 11.36% C -> A NA
LOC_Os01g71830.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71840.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 42.665; most accessible tissue: Zhenshan97 root, score: 92.529
vg0141604657 (J) chr01 41604657 A G 43.30% 13.82% A -> G,T NA
LOC_Os01g71830.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71840.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71830.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71840.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 42.555; most accessible tissue: Zhenshan97 root, score: 92.529
vg0141604660 (J) chr01 41604660 A G 43.50% 37.94% A -> G NA
LOC_Os01g71830.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71840.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 40.938; most accessible tissue: Zhenshan97 root, score: 91.881
vg0141604662 (J) chr01 41604662 TA T 43.50% 38.95% TA -> T NA
LOC_Os01g71830.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71840.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 40.843; most accessible tissue: Zhenshan97 root, score: 91.881
vg0141604664 (J) chr01 41604664 C T 43.50% 39.12% C -> T NA
LOC_Os01g71830.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71840.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 40.709; most accessible tissue: Zhenshan97 root, score: 91.559