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Gene ID/Symbol/Name (e.g., LOC_Os01g08570 or hwh1 or Os01g0180900 or gly%ltransferase, note: wildcard character '%' is also acceptable.):
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Search Results:

17 variations found. LOC_Os03g05770 (peroxidase precursor; putative; expressed), ranging from 2,878,827 bp to 2,880,890 bp (including 0 kb upstream and 0 kb downstream of the gene).

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
vg0302878869 (J) chr03 2878869 CCCT C 99.40% 0.00% CCCT -> C NA
LOC_Os03g05770.1 Alt: C| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 88.601; most accessible tissue: Zhenshan97 young leaf, score: 92.102
vg0302879144 (J) chr03 2879144 C T 96.50% 0.00% C -> T NA
LOC_Os03g05760.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g05780.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g05770.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 81.986; most accessible tissue: Minghui63 panicle, score: 88.595
vg0302879570 (J) chr03 2879570 C T 99.80% 0.00% C -> T NA
LOC_Os03g05770.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 77.349; most accessible tissue: Zhenshan97 young leaf, score: 85.184
vg0302879636 (J) chr03 2879636 C T 99.90% 0.00% C -> T NA
LOC_Os03g05770.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os03g05760.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g05780.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 75.762; most accessible tissue: Zhenshan97 young leaf, score: 87.584
vg0302880239 (J) chr03 2880239 C T 99.80% 0.00% C -> T NA
LOC_Os03g05770.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os03g05760.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g05780.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 74.942; most accessible tissue: Minghui63 panicle, score: 87.951
vg0302880347 (J) chr03 2880347 C Unkown 90.50% 1.93% C -> G NA
LOC_Os03g05770.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os03g05760.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g05780.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 69.431; most accessible tissue: Minghui63 panicle, score: 84.005
vg0302880418 (J) chr03 2880418 CGAA CGAAGAA GAAGAAG AA 56.30% 0.17% CGAAGAAGAA GAAGAA -> CGAA,CGAAG AAGAAGAAGA AGAA,CGAAG AAGAA,CGAA GAA,CGAAGA AGAAGAA,C NA
LOC_Os03g05770.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g05760.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g05780.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g05770.1 Alt: CGAAGAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g05760.1 Alt: CGAAGAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g05780.1 Alt: CGAAGAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g05770.1 Alt: CGAAGAAGAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g05760.1 Alt: CGAAGAAGAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g05780.1 Alt: CGAAGAAGAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g05770.1 Alt: CGAAGAAGAAGAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g05780.1 Alt: CGAAGAAGAAGAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g05770.1 Alt: CGAAGAAGAAGAAGAAGAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g05780.1 Alt: CGAAGAAGAAGAAGAAGAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g05770.1 Alt: CGAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g05760.1 Alt: CGAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g05780.1 Alt: CGAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 67.678; most accessible tissue: Zhenshan97 panicle, score: 81.135
vg0302880430 (J) chr03 2880430 A C 99.60% 0.00% A -> C NA
LOC_Os03g05770.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g05760.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g05780.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 69.932; most accessible tissue: Callus, score: 83.477
vg0302880474 (J) chr03 2880474 C T 99.70% 0.00% C -> T NA
LOC_Os03g05770.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g05780.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 63.485; most accessible tissue: Callus, score: 83.477
vg0302880485 (J) chr03 2880485 T C 60.40% 0.21% C -> T
mr1063 (All); LR P-value: 5.21E-48;
mr1870 (All); LR P-value: 8.08E-15;
mr1129_2 (All); LR P-value: 2.87E-37;
mr1255_2 (All); LR P-value: 5.00E-21
LOC_Os03g05770.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g05780.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 62.736; most accessible tissue: Callus, score: 83.477
vg0302880522 (J) chr03 2880522 G T 99.90% 0.00% G -> T NA
LOC_Os03g05770.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g05780.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 58.023; most accessible tissue: Callus, score: 83.477
vg0302880531 (J) chr03 2880531 ACTCT ACT 56.20% 1.48% ACT -> ACTCT,A NA
LOC_Os03g05770.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g05780.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
LOC_Os03g05770.1 Alt: ACTCT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g05780.1 Alt: ACTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 57.763; most accessible tissue: Callus, score: 83.477
vg0302880607 (J) chr03 2880607 T A 99.80% 0.00% T -> A NA
LOC_Os03g05770.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g05780.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 49.729; most accessible tissue: Callus, score: 70.114
vg0302880671 (J) chr03 2880671 C CT 60.40% 0.23% CT -> C,CTT NA
LOC_Os03g05770.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g05780.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g05770.1 Alt: CTT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g05780.1 Alt: CTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 47.660; most accessible tissue: Callus, score: 70.114
vg0302880721 (J) chr03 2880721 C T 60.50% 0.30% T -> C
mr1063 (All); LR P-value: 7.96E-49;
mr1828 (All); LR P-value: 1.42E-34;
mr1870 (All); LR P-value: 1.60E-15;
mr1088_2 (All); LR P-value: 1.94E-73;
mr1129_2 (All); LR P-value: 1.77E-37;
mr1255_2 (All); LR P-value: 7.47E-21;
mr1323_2 (All); LR P-value: 4.02E-26;
mr1404_2 (All); LR P-value: 5.48E-50
LOC_Os03g05770.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g05780.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 46.568; most accessible tissue: Callus, score: 89.101
vg0302880739 (J) chr03 2880739 T C 96.50% 0.00% T -> C NA
LOC_Os03g05770.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g05780.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 47.022; most accessible tissue: Callus, score: 89.101
STR0302879138 (J) chr03 2879138 TGCGTGC GTGCGTG T TGCGTGT GTGCGTG T 98.60% 0.00% TGCGTGCGTG CGTGT -> TGCGTGTGTG CGTGT NA