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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:

9 variations found. LOC_Os12g35660 (transposon protein; putative; CACTA; En%2FSpm sub-class; expressed), ranging from 21,679,982 bp to 21,683,377 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
vg1221680732 (J) chr12 21680732 G A 64.10% 21.77% G -> A NA
LOC_Os12g35660.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g35660.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 9.965; most accessible tissue: Minghui63 panicle, score: 16.270
vg1221681539 (J) chr12 21681539 G A 69.30% 20.63% G -> A NA
LOC_Os12g35660.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g35660.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 16.948; most accessible tissue: Zhenshan97 flag leaf, score: 28.494
vg1221681937 (J) chr12 21681937 C T 72.60% 19.23% C -> T NA
LOC_Os12g35660.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g35660.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 43.362; most accessible tissue: Minghui63 young leaf, score: 61.887
vg1221682066 (J) chr12 21682066 C T 74.30% 17.22% C -> T NA
LOC_Os12g35660.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g35660.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 42.684; most accessible tissue: Minghui63 flag leaf, score: 62.470
vg1221682087 (J) chr12 21682087 C T 72.90% 16.67% C -> T
mr1210 (Jap_All); LR P-value: 6.53E-09;
mr1222 (Jap_All); LMM P-value: 5.93E-06; LR P-value: 4.08E-06;
mr1275 (Jap_All); LMM P-value: 2.35E-06; LR P-value: 2.35E-06;
mr1284 (Jap_All); LMM P-value: 1.46E-06; LR P-value: 1.46E-06;
mr1305 (Jap_All); LR P-value: 8.94E-09;
mr1358 (Jap_All); LR P-value: 5.16E-07;
mr1359 (Jap_All); LR P-value: 4.28E-06;
mr1370 (Jap_All); LMM P-value: 1.63E-08; LR P-value: 1.63E-08;
mr1461 (Jap_All); LMM P-value: 8.18E-07; LR P-value: 8.18E-07;
mr1515 (Jap_All); LR P-value: 9.59E-07;
mr1585 (Jap_All); LR P-value: 9.94E-07;
mr1586 (Jap_All); LR P-value: 1.81E-06;
mr1788 (Jap_All); LR P-value: 5.49E-06;
mr1882 (Jap_All); LMM P-value: 7.10E-06; LR P-value: 1.66E-06;
mr1305_2 (Jap_All); LR P-value: 1.67E-06;
mr1585_2 (Jap_All); LR P-value: 1.66E-07
LOC_Os12g35660.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g35660.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 39.713; most accessible tissue: Minghui63 flag leaf, score: 55.781
vg1221682433 (J) chr12 21682433 C G 72.70% 19.09% C -> G NA
LOC_Os12g35660.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g35660.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 16.505; most accessible tissue: Minghui63 panicle, score: 29.741
vg1221682741 (J) chr12 21682741 G A 0.50% 62.53% A -> G NA
LOC_Os12g35660.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g35660.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 6.152; most accessible tissue: Zhenshan97 flower, score: 11.396
vg1221683046 (J) chr12 21683046 G A 9.30% 52.84% G -> A NA
LOC_Os12g35660.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g35660.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 12.187; most accessible tissue: Zhenshan97 panicle, score: 20.424
vg1221683047 (J) chr12 21683047 C A 5.70% 51.27% C -> A NA
LOC_Os12g35660.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g35660.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 12.187; most accessible tissue: Zhenshan97 panicle, score: 20.424