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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:

22 variations found. LOC_Os01g67990 (transposon protein; putative; unclassified; expressed), ranging from 39,512,259 bp to 39,514,988 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
vg0139512288 (J) chr01 39512288 C T 26.70% 72.32% C -> T NA
LOC_Os01g67990.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g67990.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 7.548; most accessible tissue: Callus, score: 21.029
vg0139512311 (J) chr01 39512311 G A 39.20% 49.68% G -> A NA
LOC_Os01g67990.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g67990.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 7.472; most accessible tissue: Callus, score: 21.029
vg0139512336 (J) chr01 39512336 C T 45.40% 47.04% C -> T NA
LOC_Os01g67990.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os01g67990.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.421; most accessible tissue: Zhenshan97 root, score: 12.891
vg0139512419 (J) chr01 39512419 G A 29.10% 63.88% G -> A NA
LOC_Os01g67990.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g67990.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.789; most accessible tissue: Zhenshan97 root, score: 16.934
vg0139512426 (J) chr01 39512426 T C 28.10% 68.22% T -> C NA
LOC_Os01g67990.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g67990.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 7.020; most accessible tissue: Zhenshan97 root, score: 16.934
vg0139512433 (J) chr01 39512433 T C 26.20% 70.21% T -> C NA
LOC_Os01g67990.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g67990.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 7.020; most accessible tissue: Zhenshan97 root, score: 16.934
vg0139512435 (J) chr01 39512435 T C 27.30% 71.90% T -> C NA
LOC_Os01g67990.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g67990.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 7.020; most accessible tissue: Zhenshan97 root, score: 16.934
vg0139512481 (J) chr01 39512481 T C 26.40% 70.40% T -> C NA
LOC_Os01g67990.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g67990.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 9.153; most accessible tissue: Zhenshan97 root, score: 18.731
vg0139512492 (J) chr01 39512492 C A 27.50% 71.39% C -> A NA
LOC_Os01g67990.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os01g67990.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 9.347; most accessible tissue: Zhenshan97 root, score: 18.731
vg0139512590 (J) chr01 39512590 G A 10.00% 76.66% G -> A NA
LOC_Os01g67990.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g67990.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 10.696; most accessible tissue: Zhenshan97 root, score: 20.427
vg0139512853 (J) chr01 39512853 C A 26.20% 71.75% C -> A NA
LOC_Os01g67990.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g67990.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 11.966; most accessible tissue: Zhenshan97 root, score: 16.934
vg0139512862 (J) chr01 39512862 G C 26.20% 71.84% G -> C NA
LOC_Os01g67990.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g67990.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 11.812; most accessible tissue: Zhenshan97 root, score: 16.934
vg0139512926 (J) chr01 39512926 C T 25.30% 72.87% C -> T NA
LOC_Os01g67990.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g67990.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 11.257; most accessible tissue: Callus, score: 20.750
vg0139513349 (J) chr01 39513349 C T 25.30% 72.96% C -> T NA
LOC_Os01g67990.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g67990.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.529; most accessible tissue: Minghui63 root, score: 17.665
vg0139513400 (J) chr01 39513400 A G 8.90% 77.42% A -> G NA
LOC_Os01g67990.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g67990.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.529; most accessible tissue: Minghui63 root, score: 17.665
vg0139513555 (J) chr01 39513555 C T 26.70% 72.34% C -> T NA
LOC_Os01g67990.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g67990.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.540; most accessible tissue: Callus, score: 16.271
vg0139513562 (J) chr01 39513562 T G 26.20% 71.67% T -> G NA
LOC_Os01g67990.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g67990.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.540; most accessible tissue: Callus, score: 16.271
vg0139513841 (J) chr01 39513841 G A 25.30% 71.43% G -> A NA
LOC_Os01g67990.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os01g67990.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.876; most accessible tissue: Callus, score: 26.099
vg0139513862 (J) chr01 39513862 T C 25.70% 72.30% T -> C NA
LOC_Os01g67990.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g67990.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 6.876; most accessible tissue: Callus, score: 26.099
vg0139513874 (J) chr01 39513874 G A 26.30% 71.52% G -> A NA
LOC_Os01g67990.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os01g67990.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.876; most accessible tissue: Callus, score: 26.099
vg0139513943 (J) chr01 39513943 G A 26.00% 71.90% G -> A NA
LOC_Os01g67990.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g67990.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 7.208; most accessible tissue: Callus, score: 29.745
vg0139514069 (J) chr01 39514069 C T 20.20% 73.25% C -> T
mr1347_2 (Jap_All); LR P-value: 8.94E-07;
mr1696_2 (All); LR P-value: 4.07E-07
LOC_Os01g67990.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g67990.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 7.124; most accessible tissue: Callus, score: 29.745