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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:

26 variations found. LOC_Os12g15770 (retrotransposon protein; putative; Ty3-gypsy subclass), ranging from 9,004,280 bp to 9,004,637 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
vg1209004310 (J) chr12 9004310 C T 78.60% 20.33% C -> T NA
LOC_Os12g15770.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g15770.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 40.672; most accessible tissue: Callus, score: 70.638
vg1209004311 (J) chr12 9004311 A G 39.60% 21.88% G -> A
mr1425 (All); LR P-value: 1.91E-08;
mr1659 (All); LR P-value: 6.85E-08;
mr1864_2 (Ind_All); LR P-value: 1.04E-06
LOC_Os12g15770.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g15770.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 40.717; most accessible tissue: Callus, score: 70.638
vg1209004330 (J) chr12 9004330 T G 39.80% 21.54% G -> T
mr1425 (All); LR P-value: 9.03E-09;
mr1425 (Ind_All); LR P-value: 2.92E-06;
mr1574 (All); LR P-value: 3.19E-06;
mr1659 (All); LR P-value: 3.50E-08;
mr1864_2 (Ind_All); LR P-value: 4.06E-06
LOC_Os12g15770.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g15770.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 39.483; most accessible tissue: Minghui63 flag leaf, score: 69.182
vg1209004353 (J) chr12 9004353 T C 39.80% 21.58% C -> T
mr1425 (All); LR P-value: 2.05E-08;
mr1659 (All); LR P-value: 7.24E-08;
mr1864_2 (Ind_All); LR P-value: 3.38E-06
LOC_Os12g15770.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g15770.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 39.365; most accessible tissue: Zhenshan97 young leaf, score: 68.794
vg1209004381 (J) chr12 9004381 C T 78.80% 20.25% C -> T NA
LOC_Os12g15770.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g15770.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 39.482; most accessible tissue: Minghui63 young leaf, score: 66.656
vg1209004386 (J) chr12 9004386 A C 77.70% 20.23% A -> C NA
LOC_Os12g15770.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os12g15770.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 39.813; most accessible tissue: Minghui63 young leaf, score: 66.656
vg1209004409 (J) chr12 9004409 T C 39.80% 21.67% C -> T
mr1425 (All); LR P-value: 7.08E-08;
mr1659 (All); LR P-value: 1.54E-07
LOC_Os12g15770.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g15770.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 40.633; most accessible tissue: Zhenshan97 young leaf, score: 69.263
vg1209004418 (J) chr12 9004418 G A 39.70% 21.71% A -> G
mr1425 (All); LR P-value: 2.67E-08;
mr1659 (All); LR P-value: 1.84E-07
LOC_Os12g15770.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g15770.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 40.821; most accessible tissue: Zhenshan97 young leaf, score: 69.723
vg1209004419 (J) chr12 9004419 T C 79.30% 18.98% T -> C NA
LOC_Os12g15770.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os12g15770.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 40.772; most accessible tissue: Zhenshan97 young leaf, score: 69.723
vg1209004478 (J) chr12 9004478 C T 39.80% 21.71% T -> C
mr1425 (All); LR P-value: 1.47E-07;
mr1864_2 (Ind_All); LR P-value: 8.41E-06
LOC_Os12g15770.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os12g15770.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 44.259; most accessible tissue: Callus, score: 82.589
vg1209004488 (J) chr12 9004488 C T 39.70% 21.94% T -> C
mr1425 (All); LR P-value: 1.53E-08;
mr1659 (All); LR P-value: 1.01E-07
LOC_Os12g15770.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os12g15770.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 44.166; most accessible tissue: Callus, score: 82.589
vg1209004497 (J) chr12 9004497 C T 78.20% 20.65% C -> T NA
LOC_Os12g15770.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g15770.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 44.613; most accessible tissue: Callus, score: 82.589
vg1209004514 (J) chr12 9004514 C T 77.70% 20.69% C -> T NA
LOC_Os12g15770.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g15770.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 44.872; most accessible tissue: Callus, score: 82.589
vg1209004523 (J) chr12 9004523 C G 71.40% 21.12% C -> G
mr1305 (All); LR P-value: 1.39E-24;
mr1586 (All); LR P-value: 2.77E-24
LOC_Os12g15770.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g15770.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 45.147; most accessible tissue: Callus, score: 82.589
vg1209004531 (J) chr12 9004531 A G 78.60% 20.63% A -> G NA
LOC_Os12g15770.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g15770.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 45.395; most accessible tissue: Callus, score: 82.589
vg1209004534 (J) chr12 9004534 G A 75.70% 20.76% G -> A NA
LOC_Os12g15770.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g15770.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 44.747; most accessible tissue: Callus, score: 82.589
vg1209004546 (J) chr12 9004546 T C 39.70% 21.67% C -> T
mr1425 (All); LR P-value: 4.22E-09;
mr1425 (Ind_All); LR P-value: 1.43E-06;
mr1574 (All); LR P-value: 4.45E-06;
mr1659 (All); LR P-value: 1.54E-07
LOC_Os12g15770.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g15770.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 46.019; most accessible tissue: Callus, score: 82.589
vg1209004550 (J) chr12 9004550 C T 78.60% 20.74% C -> T NA
LOC_Os12g15770.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g15770.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 46.249; most accessible tissue: Callus, score: 82.589
vg1209004551 (J) chr12 9004551 G T 78.60% 20.76% G -> T NA
LOC_Os12g15770.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g15770.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 46.249; most accessible tissue: Callus, score: 82.589
vg1209004584 (J) chr12 9004584 G C 77.10% 21.22% G -> C NA
LOC_Os12g15770.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os12g15770.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 46.048; most accessible tissue: Minghui63 flag leaf, score: 76.453
vg1209004589 (J) chr12 9004589 T C 39.60% 21.94% C -> T
mr1425 (All); LR P-value: 3.41E-10;
mr1425 (Ind_All); LR P-value: 1.14E-08;
mr1574 (All); LR P-value: 1.62E-06;
mr1539_2 (Ind_All); LR P-value: 7.47E-06;
mr1540_2 (Ind_All); LR P-value: 4.75E-07;
mr1732_2 (Ind_All); LR P-value: 3.55E-06;
mr1864_2 (Ind_All); LR P-value: 1.53E-07;
mr1882_2 (All); LR P-value: 5.59E-07
LOC_Os12g15770.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g15770.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 46.902; most accessible tissue: Minghui63 flag leaf, score: 77.828
vg1209004590 (J) chr12 9004590 C T 39.80% 21.71% T -> C
mr1425 (All); LR P-value: 3.61E-08;
mr1425 (Ind_All); LR P-value: 2.84E-06;
mr1864_2 (Ind_All); LR P-value: 9.45E-06
LOC_Os12g15770.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os12g15770.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 46.847; most accessible tissue: Minghui63 flag leaf, score: 77.828
vg1209004601 (J) chr12 9004601 AAT A 48.60% 21.52% AAT -> A NA
LOC_Os12g15770.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g15770.1 Alt: A| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 46.494; most accessible tissue: Minghui63 flag leaf, score: 77.494
vg1209004619 (J) chr12 9004619 A G 68.60% 20.97% A -> G NA
LOC_Os12g15770.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g15770.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 45.713; most accessible tissue: Minghui63 flag leaf, score: 76.091
vg1209004623 (J) chr12 9004623 C G 77.90% 20.78% C -> G NA
LOC_Os12g15770.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g15770.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 45.163; most accessible tissue: Minghui63 flag leaf, score: 74.563
vg1209004627 (J) chr12 9004627 A T 78.50% 20.82% A -> T NA
LOC_Os12g15770.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g15770.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 44.861; most accessible tissue: Minghui63 flag leaf, score: 73.752