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Search Results:

15 variations found. LOC_Os04g46780 (MSP domain containing protein; expressed), ranging from 27,732,605 bp to 27,735,793 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
vg0427732885 (J) chr04 27732885 G Unkown 54.20% 27.32% G -> A NA
LOC_Os04g46780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g46780.2 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g46780.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os04g46780.2 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os04g46760.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os04g46770.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os04g46790.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 75.114; most accessible tissue: Zhenshan97 root, score: 86.685
vg0427734012 (J) chr04 27734012 T A 80.40% 0.00% T -> A
mr1031 (Ind_All); LR P-value: 2.42E-06;
mr1035 (Ind_All); LR P-value: 8.98E-07;
mr1050 (Ind_All); LR P-value: 9.14E-07;
mr1155 (Ind_All); LR P-value: 5.83E-06;
mr1169 (Ind_All); LR P-value: 6.72E-06;
mr1174 (All); LR P-value: 8.30E-08;
mr1174 (Ind_All); LR P-value: 2.00E-08;
mr1193 (All); LR P-value: 6.77E-07;
mr1291 (All); LR P-value: 1.12E-06;
mr1354 (Ind_All); LR P-value: 1.07E-07;
mr1626 (Ind_All); LR P-value: 9.68E-07;
mr1709 (All); LR P-value: 9.76E-07;
mr1798 (Ind_All); LR P-value: 3.37E-06;
mr1035_2 (Ind_All); LMM P-value: 2.07E-06; LR P-value: 2.07E-06;
mr1158_2 (All); LR P-value: 5.89E-06;
mr1170_2 (All); LR P-value: 3.23E-08;
mr1174_2 (Ind_All); LR P-value: 7.08E-08;
mr1354_2 (Ind_All); LR P-value: 1.01E-08;
mr1458_2 (Ind_All); LR P-value: 5.12E-07;
mr1631_2 (Ind_All); LR P-value: 3.63E-07;
mr1715_2 (Ind_All); LR P-value: 6.61E-11;
mr1720_2 (Ind_All); LR P-value: 3.20E-07;
mr1733_2 (Ind_All); LR P-value: 5.15E-06;
mr1895_2 (Ind_All); LR P-value: 4.58E-07;
mr1904_2 (Ind_All); LR P-value: 1.00E-06;
mr1928_2 (All); LR P-value: 9.61E-06;
mr1931_2 (All); LR P-value: 3.21E-08;
mr1931_2 (Ind_All); LR P-value: 6.28E-08;
mr1942_2 (Ind_All); LR P-value: 2.47E-06
LOC_Os04g46780.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46800.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46770.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46790.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46780.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 50.620; most accessible tissue: Callus, score: 82.952
vg0427734065 (J) chr04 27734065 C T 65.70% 0.00% C -> T
mr1174 (Ind_All); LR P-value: 2.22E-07;
mr1298 (Ind_All); LR P-value: 7.00E-06;
mr1731 (Ind_All); LR P-value: 6.00E-07;
mr1174_2 (Ind_All); LR P-value: 7.80E-09;
mr1347_2 (Ind_All); LR P-value: 3.39E-08;
mr1355_2 (All); LR P-value: 5.70E-06
LOC_Os04g46780.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46800.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46770.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46790.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46780.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 50.760; most accessible tissue: Callus, score: 82.952
vg0427734139 (J) chr04 27734139 A G 65.70% 0.38% A -> G
mr1174 (Ind_All); LR P-value: 7.10E-08;
mr1731 (Ind_All); LR P-value: 4.39E-07;
mr1174_2 (Ind_All); LR P-value: 3.17E-09;
mr1347_2 (Ind_All); LR P-value: 3.21E-08;
mr1355_2 (All); LR P-value: 3.52E-06
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g46780.2 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46800.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46770.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46790.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46780.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 52.795; most accessible tissue: Zhenshan97 root, score: 75.275
vg0427734251 (J) chr04 27734251 A C 65.90% 0.08% A -> C
mr1174 (Ind_All); LR P-value: 3.72E-08;
mr1731 (Ind_All); LR P-value: 5.71E-07;
mr1174_2 (Ind_All); LR P-value: 2.76E-09;
mr1347_2 (Ind_All); LR P-value: 2.09E-08;
mr1354_2 (Ind_All); LR P-value: 7.21E-06;
mr1355_2 (All); LR P-value: 3.98E-06
LOC_Os04g46780.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46800.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46770.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46790.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46780.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 53.558; most accessible tissue: Callus, score: 86.140
vg0427734444 (J) chr04 27734444 G C 53.90% 0.08% C -> G
mr1873 (Ind_All); LR P-value: 2.34E-06;
mr1329_2 (All); LR P-value: 3.60E-06;
mr1336_2 (All); LR P-value: 1.42E-18;
mr1579_2 (All); LR P-value: 4.88E-16;
mr1690_2 (All); LR P-value: 1.73E-08;
mr1745_2 (Ind_All); LR P-value: 4.00E-07
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g46780.2 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46800.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46770.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46790.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46780.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 54.865; most accessible tissue: Callus, score: 83.736
vg0427734589 (J) chr04 27734589 C T 80.20% 0.30% C -> T
mr1013 (Ind_All); LR P-value: 8.83E-06;
mr1031 (Ind_All); LR P-value: 1.71E-06;
mr1035 (Ind_All); LR P-value: 3.24E-06;
mr1050 (Ind_All); LR P-value: 3.40E-07;
mr1155 (Ind_All); LR P-value: 7.85E-06;
mr1163 (Ind_All); LR P-value: 5.55E-06;
mr1174 (Ind_All); LR P-value: 9.05E-08;
mr1193 (All); LR P-value: 1.17E-07;
mr1291 (All); LR P-value: 1.59E-06;
mr1354 (Ind_All); LR P-value: 9.53E-08;
mr1502 (Ind_All); LR P-value: 5.91E-06;
mr1626 (Ind_All); LR P-value: 1.67E-06;
mr1709 (All); LR P-value: 1.88E-07;
mr1709 (Ind_All); LR P-value: 8.88E-07;
mr1733 (Ind_All); LR P-value: 8.40E-06;
mr1798 (Ind_All); LR P-value: 1.99E-06;
mr1035_2 (Ind_All); LMM P-value: 2.10E-06; LR P-value: 2.10E-06;
mr1158_2 (All); LR P-value: 1.34E-06;
mr1167_2 (Ind_All); LR P-value: 5.19E-07;
mr1170_2 (All); LR P-value: 3.72E-08;
mr1174_2 (Ind_All); LR P-value: 2.51E-07;
mr1272_2 (Ind_All); LR P-value: 6.97E-06;
mr1354_2 (Ind_All); LR P-value: 1.28E-08;
mr1355_2 (Ind_All); LR P-value: 3.93E-06;
mr1439_2 (Ind_All); LR P-value: 8.69E-06;
mr1449_2 (Ind_All); LR P-value: 4.71E-06;
mr1458_2 (Ind_All); LR P-value: 3.47E-07;
mr1478_2 (Ind_All); LR P-value: 2.71E-06;
mr1631_2 (Ind_All); LR P-value: 7.04E-07;
mr1715_2 (All); LR P-value: 4.99E-16;
mr1715_2 (Ind_All); LR P-value: 2.07E-12;
mr1719_2 (Ind_All); LR P-value: 6.40E-06;
mr1720_2 (Ind_All); LR P-value: 1.07E-07;
mr1733_2 (Ind_All); LR P-value: 1.76E-06;
mr1895_2 (Ind_All); LR P-value: 6.13E-08;
mr1904_2 (Ind_All); LR P-value: 1.64E-07;
mr1931_2 (All); LR P-value: 2.48E-08;
mr1931_2 (Ind_All); LR P-value: 6.24E-08;
mr1942_2 (Ind_All); LR P-value: 9.23E-07
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g46800.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46770.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46790.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46780.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46780.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 43.569; most accessible tissue: Zhenshan97 young leaf, score: 55.899
vg0427734612 (J) chr04 27734612 T C 54.00% 0.00% C -> T
mr1873 (Ind_All); LR P-value: 8.75E-06;
mr1329_2 (All); LR P-value: 9.75E-06;
mr1336_2 (All); LR P-value: 1.24E-18;
mr1579_2 (All); LR P-value: 9.08E-16;
mr1690_2 (All); LR P-value: 3.42E-08;
mr1745_2 (Ind_All); LR P-value: 3.03E-07;
mr1873_2 (All); LR P-value: 4.79E-32
LOC_Os04g46800.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46770.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46790.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46780.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46780.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 42.807; most accessible tissue: Zhenshan97 young leaf, score: 56.533
vg0427734835 (J) chr04 27734835 A G 53.80% 0.02% G -> A
mr1873 (Ind_All); LR P-value: 2.34E-06;
mr1329_2 (All); LR P-value: 3.60E-06;
mr1336_2 (All); LR P-value: 1.42E-18;
mr1579_2 (All); LR P-value: 4.88E-16;
mr1690_2 (All); LR P-value: 1.73E-08;
mr1745_2 (Ind_All); LR P-value: 4.00E-07
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g46800.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46770.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46790.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46780.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46780.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 41.381; most accessible tissue: Callus, score: 65.389
vg0427734931 (J) chr04 27734931 T C 54.00% 0.04% C -> T
mr1873 (All); LR P-value: 1.69E-39;
mr1873 (Ind_All); LR P-value: 2.34E-06;
mr1329_2 (All); LR P-value: 3.57E-06;
mr1336_2 (All); LR P-value: 1.22E-18;
mr1579_2 (All); LR P-value: 5.40E-16;
mr1690_2 (All); LR P-value: 1.73E-08;
mr1745_2 (Ind_All); LR P-value: 4.00E-07;
mr1873_2 (All); LR P-value: 7.21E-32
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g46800.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46770.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46790.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46780.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46780.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 46.082; most accessible tissue: Callus, score: 87.686
vg0427734968 (J) chr04 27734968 T G 69.30% 0.25% G -> T
mr1657 (Jap_All); LR P-value: 5.92E-06;
mr1993 (All); LR P-value: 1.45E-06
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g46800.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46770.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46790.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46780.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46780.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 46.939; most accessible tissue: Callus, score: 87.686
vg0427735043 (J) chr04 27735043 A G 99.60% 0.00% A -> G NA
LOC_Os04g46800.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os04g46770.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
LOC_Os04g46790.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
LOC_Os04g46780.1 Alt: G| intron_variant MODIFIER(snpEff)
LOC_Os04g46780.2 Alt: G| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 46.627; most accessible tissue: Callus, score: 87.686
vg0427735045 (J) chr04 27735045 G A 99.60% 0.00% G -> A NA
LOC_Os04g46800.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os04g46770.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os04g46790.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os04g46780.1 Alt: A| intron_variant MODIFIER(snpEff)
LOC_Os04g46780.2 Alt: A| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 45.566; most accessible tissue: Callus, score: 87.686
vg0427735691 (J) chr04 27735691 A T 53.80% 0.34% T -> A
mr1336_2 (All); LR P-value: 3.42E-18;
mr1579_2 (All); LR P-value: 2.74E-15;
mr1690_2 (All); LR P-value: 4.75E-08;
mr1745_2 (Ind_All); LR P-value: 2.50E-07
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g46780.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46780.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46800.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46810.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46770.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46790.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 50.705; most accessible tissue: Callus, score: 93.334
STR0427734011 (J) chr04 27734011 TTAAAAA ATATT TAAAAAA ATATT 62.50% 0.00% TTAAAAAATA TT -> TAAAAAAATA TT NA