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Search Results:

23 variations found. LOC_Os11g10840 (expressed protein), ranging from 5,974,319 bp to 5,974,523 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
vg1105974344 (J) chr11 5974344 C T 95.10% 0.36% C -> T
mr1236 (Jap_All); LR P-value: 4.10E-06;
mr1248 (Jap_All); LR P-value: 1.57E-10;
mr1522_2 (All); LR P-value: 4.59E-06
LOC_Os11g10840.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os11g10840.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 20.680; most accessible tissue: Callus, score: 34.526
vg1105974350 (J) chr11 5974350 A G 94.40% 1.52% A -> G NA
LOC_Os11g10840.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g10840.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 20.775; most accessible tissue: Callus, score: 34.526
vg1105974351 (J) chr11 5974351 G T 95.20% 0.34% G -> T
mr1236 (Jap_All); LR P-value: 4.10E-06;
mr1248 (Jap_All); LR P-value: 1.57E-10;
mr1522_2 (All); LR P-value: 4.59E-06
LOC_Os11g10840.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os11g10840.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 20.775; most accessible tissue: Callus, score: 34.526
vg1105974370 (J) chr11 5974370 G C 50.10% 0.17% C -> G NA
LOC_Os11g10840.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g10840.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 23.159; most accessible tissue: Callus, score: 34.526
vg1105974373 (J) chr11 5974373 C T 92.30% 0.06% C -> T NA
LOC_Os11g10840.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g10840.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 23.554; most accessible tissue: Callus, score: 34.526
vg1105974381 (J) chr11 5974381 T C 91.00% 4.32% T -> C NA
LOC_Os11g10840.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g10840.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 24.362; most accessible tissue: Callus, score: 34.526
vg1105974391 (J) chr11 5974391 G C 34.80% 22.11% G -> C NA
LOC_Os11g10840.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g10840.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 24.489; most accessible tissue: Callus, score: 34.526
vg1105974413 (J) chr11 5974413 G A 54.10% 43.38% G -> A NA
LOC_Os11g10840.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os11g10840.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 29.814; most accessible tissue: Minghui63 root, score: 40.262
vg1105974420 (J) chr11 5974420 C T 49.70% 43.50% C -> T NA
LOC_Os11g10840.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os11g10840.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 29.982; most accessible tissue: Minghui63 root, score: 40.262
vg1105974430 (J) chr11 5974430 T C 46.50% 49.94% T -> C NA
LOC_Os11g10840.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g10840.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 33.674; most accessible tissue: Callus, score: 75.127
vg1105974431 (J) chr11 5974431 C T 38.10% 49.05% C -> T NA
LOC_Os11g10840.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os11g10840.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 33.674; most accessible tissue: Callus, score: 75.127
vg1105974434 (J) chr11 5974434 C T 40.20% 54.40% C -> T NA
LOC_Os11g10840.1 Alt: T| missense_variant MODERATE(snpEff)/synonymous_codon(CooVar)
LOC_Os11g10840.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 33.674; most accessible tissue: Callus, score: 75.127
vg1105974435 (J) chr11 5974435 TCG T 41.60% 45.30% TCG -> T NA
LOC_Os11g10840.1 Alt: T| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os11g10840.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 33.674; most accessible tissue: Callus, score: 75.127
vg1105974436 (J) chr11 5974436 C G 50.30% 49.09% C -> G NA
LOC_Os11g10840.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g10840.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 33.674; most accessible tissue: Callus, score: 75.127
vg1105974439 (J) chr11 5974439 G A 44.40% 44.82% G -> A NA
LOC_Os11g10840.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g10840.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 33.730; most accessible tissue: Callus, score: 75.127
vg1105974446 (J) chr11 5974446 T C 51.20% 46.61% T -> G,C NA
LOC_Os11g10840.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g10840.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os11g10830.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os11g10850.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os11g10820.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
LOC_Os11g10840.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 33.730; most accessible tissue: Callus, score: 75.127
vg1105974474 (J) chr11 5974474 G A 48.10% 45.98% G -> A NA
LOC_Os11g10840.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g10840.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 38.814; most accessible tissue: Callus, score: 75.127
vg1105974479 (J) chr11 5974479 G A 48.90% 47.65% G -> A NA
LOC_Os11g10840.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os11g10840.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 38.814; most accessible tissue: Callus, score: 75.127
vg1105974491 (J) chr11 5974491 G A 49.00% 47.65% G -> A NA
LOC_Os11g10840.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g10840.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 41.187; most accessible tissue: Callus, score: 75.127
vg1105974506 (J) chr11 5974506 G C 95.70% 1.21% G -> C NA
LOC_Os11g10840.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g10840.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 45.682; most accessible tissue: Callus, score: 75.127
vg1105974508 (J) chr11 5974508 C T 50.00% 48.96% C -> T NA
LOC_Os11g10840.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g10840.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 45.682; most accessible tissue: Callus, score: 75.127
vg1105974510 (J) chr11 5974510 G A 34.60% 49.77% G -> A NA
LOC_Os11g10840.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g10840.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 45.682; most accessible tissue: Callus, score: 75.127
vg1105974521 (J) chr11 5974521 T TAGCTAG CACGG 49.60% 0.76% T -> TAGCTAGCAC GG NA
LOC_Os11g10840.1 Alt: TAGCTAGCACGG| frameshift_variant&stop_gained HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os11g10840.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 46.673; most accessible tissue: Callus, score: 75.127