20 variations found. Os02g0527900/LOC_Os02g32620 (PAN domain-containing protein At5g03700 precursor; putative; expressed), ranging from 19,342,026 bp to 19,343,736 bp (including 0 kb upstream and 0 kb downstream of the gene).
Gene ID | Annotation |
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LOC_Os02g32620 | PAN domain-containing protein At5g03700 precursor, putative, expressed; RAP ID: Os02g0527900; MSU ID: LOC_Os02g32620 |
The expression data is from the CREP database. And the expression value is log2-transformed. Move the mouse over the cells of the heat map to get detailed tissue information and expression values.
Color | Explain | Details |
---|---|---|
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. |
Var ID | Chrom | Position | Primary Allele | Secondary Allele | Primary Allele Frequency | DEL Frequency | Var | GWAS Results | Effect |
---|---|---|---|---|---|---|---|---|---|
vg0219342066 (J) | chr02 | 19342066 | C | CTCT | 58.90% | 0.38% | C -> CTCTTCT,CT CTTCTTCTTC TTCTTCTTCT ,CTCT,CTCT TCTTCTTCTT CTTCTTCTTC T,CTCTTCGT CTTCTTCTTC TTCTTCT,CT CTTCGTCTTC TTCTTCTTCT | NA |
LOC_Os02g32620.1 Alt: CTCTTCTTCTTCTTCTTCTTCTTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g32630.1 Alt: CTCTTCTTCTTCTTCTTCTTCTTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os02g32620.1 Alt: CTCTTCTTCTTCTTCTTCTTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g32630.1 Alt: CTCTTCTTCTTCTTCTTCTTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g32620.1 Alt: CTCTTCGTCTTCTTCTTCTTCTTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g32630.1 Alt: CTCTTCGTCTTCTTCTTCTTCTTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g32620.1 Alt: CTCTTCGTCTTCTTCTTCTTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g32630.1 Alt: CTCTTCGTCTTCTTCTTCTTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g32620.1 Alt: CTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g32630.1 Alt: CTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g32620.1 Alt: CTCTTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g32630.1 Alt: CTCTTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 92.370; most accessible tissue: Minghui63 root, score: 98.094 |
vg0219342069 (J) | chr02 | 19342069 | T | TTCG | 94.20% | 0.00% | T -> TTCG | NA |
LOC_Os02g32620.1 Alt: TTCG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g32630.1 Alt: TTCG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 92.290; most accessible tissue: Minghui63 root, score: 98.050 |
vg0219342072 (J) | chr02 | 19342072 | T | G | 69.40% | 18.83% | T -> G | NA |
LOC_Os02g32620.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g32630.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 92.260; most accessible tissue: Minghui63 root, score: 98.028 |
vg0219342098 (J) | chr02 | 19342098 | C | CTTCTTC TTCTTCT TCTTCTT | 96.50% | 0.99% | C -> CTTCTTCTTC TTCTTCTTCT T,CTTCTTCT TCTTCTTCTT ,CTTCTTCTT CTTCTT,CTT CTTCTT,CTT CTTCTTCTT, CTTCTTCTTC TTCTTCTTCT TCTT | NA |
LOC_Os02g32620.1 Alt: CTTCTTCTTCTTCTTCTTCTTCTT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g32630.1 Alt: CTTCTTCTTCTTCTTCTTCTTCTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os02g32620.1 Alt: CTTCTTCTTCTTCTTCTT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g32630.1 Alt: CTTCTTCTTCTTCTTCTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g32620.1 Alt: CTTCTTCTTCTTCTTCTTCTT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g32630.1 Alt: CTTCTTCTTCTTCTTCTTCTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g32620.1 Alt: CTTCTTCTTCTT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g32630.1 Alt: CTTCTTCTTCTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g32620.1 Alt: CTTCTTCTTCTTCTT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g32630.1 Alt: CTTCTTCTTCTTCTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g32620.1 Alt: CTTCTTCTT| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os02g32630.1 Alt: CTTCTTCTT| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 90.072; most accessible tissue: Minghui63 root, score: 97.617 |
vg0219342099 (J) | chr02 | 19342099 | C | T | 85.20% | 7.55% | C -> T | NA |
LOC_Os02g32620.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g32630.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 90.129; most accessible tissue: Minghui63 root, score: 97.617 |
vg0219342149 (J) | chr02 | 19342149 | C | G | 51.80% | 0.59% | G -> C |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os02g32620.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g32630.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 90.218; most accessible tissue: Minghui63 root, score: 96.882 |
|
vg0219342248 (J) | chr02 | 19342248 | TGCGGCG GCGGCG | T | 50.40% | 0.00% | TGCGGCGGCG GCG -> T,TGCGGCGG CGGCGGCG,T GCG | NA |
LOC_Os02g32620.1 Alt: T| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os02g32620.1 Alt: TGCGGCGGCGGCGGCG| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) LOC_Os02g32620.1 Alt: TGCG| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 90.699; most accessible tissue: Zhenshan97 flag leaf, score: 94.746 |
vg0219342361 (J) | chr02 | 19342361 | C | G | 65.90% | 0.11% | C -> G |
Plant_height (All); LR P-value: 2.43E-19;
mr1151 (All); LR P-value: 5.25E-10; mr1180 (All); LR P-value: 4.62E-13; mr1180 (Ind_All); LR P-value: 4.59E-07; mr1183 (All); LR P-value: 5.00E-16; mr1503 (All); LR P-value: 1.27E-16; mr1627 (Ind_All); LR P-value: 6.46E-07; mr1881 (All); LR P-value: 3.46E-06; mr1041_2 (All); LR P-value: 2.86E-06; mr1084_2 (All); LR P-value: 7.85E-08; mr1180_2 (All); LR P-value: 2.87E-21; mr1180_2 (Ind_All); LR P-value: 1.16E-08; mr1183_2 (All); LR P-value: 6.24E-25; mr1183_2 (Ind_All); LR P-value: 3.07E-08; mr1215_2 (All); LR P-value: 6.63E-09; mr1220_2 (All); LR P-value: 2.67E-11; mr1294_2 (All); LR P-value: 5.44E-06; mr1319_2 (All); LR P-value: 3.70E-09; mr1330_2 (All); LR P-value: 1.90E-13; mr1360_2 (All); LR P-value: 2.86E-06; mr1360_2 (Ind_All); LR P-value: 5.74E-06; mr1376_2 (All); LR P-value: 1.27E-07; mr1378_2 (Ind_All); LR P-value: 7.88E-07; mr1386_2 (Ind_All); LR P-value: 7.34E-06; mr1431_2 (All); LR P-value: 1.21E-07; mr1604_2 (All); LR P-value: 5.93E-07; mr1627_2 (All); LR P-value: 1.46E-25; mr1627_2 (Ind_All); LR P-value: 6.60E-13; mr1794_2 (All); LR P-value: 3.27E-15; mr1885_2 (All); LR P-value: 1.56E-07 |
LOC_Os02g32620.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g32620.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 88.217; most accessible tissue: Zhenshan97 flag leaf, score: 95.693 |
vg0219342438 (J) | chr02 | 19342438 | C | A | 56.60% | 0.32% | A -> C |
LOC_Os02g32620.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g32620.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 90.489; most accessible tissue: Zhenshan97 flag leaf, score: 95.494 |
|
vg0219342441 (J) | chr02 | 19342441 | G | T | 56.60% | 0.32% | T -> G |
LOC_Os02g32620.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g32620.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 90.449; most accessible tissue: Zhenshan97 flag leaf, score: 95.494 |
|
vg0219342492 (J) | chr02 | 19342492 | G | A | 82.00% | 0.00% | G -> A |
mr1063 (Ind_All); LR P-value: 9.13E-06;
mr1213 (Jap_All); LR P-value: 8.02E-06; mr1215 (Ind_All); LR P-value: 6.78E-06; mr1460 (Ind_All); LMM P-value: 2.52E-06; LR P-value: 2.52E-06; mr1215_2 (Ind_All); LR P-value: 7.46E-06; mr1220_2 (Ind_All); LR P-value: 6.05E-06; mr1381_2 (Ind_All); LR P-value: 8.64E-06; mr1661_2 (Ind_All); LR P-value: 5.10E-07; mr1696_2 (Ind_All); LR P-value: 3.65E-06 |
LOC_Os02g32620.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 91.056; most accessible tissue: Zhenshan97 flag leaf, score: 95.925 |
vg0219342827 (J) | chr02 | 19342827 | G | A | 51.90% | 0.00% | A -> G |
mr1213 (Jap_All); LR P-value: 4.65E-06;
mr1224 (Jap_All); LR P-value: 6.12E-06; mr1610 (All); LR P-value: 8.85E-08; mr1180_2 (All); LR P-value: 1.42E-15; mr1180_2 (Ind_All); LR P-value: 1.08E-06; mr1543_2 (Ind_All); LR P-value: 8.14E-06; mr1627_2 (Ind_All); LR P-value: 1.81E-08; mr1851_2 (All); LR P-value: 3.31E-09; mr1885_2 (All); LR P-value: 1.39E-07 |
LOC_Os02g32620.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 90.789; most accessible tissue: Zhenshan97 young leaf, score: 96.130 |
vg0219342947 (J) | chr02 | 19342947 | A | C | 99.80% | 0.00% | A -> C,G | NA |
LOC_Os02g32620.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os02g32630.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g32620.1 Alt: C| synonymous_variant LOW(snpEff) LOC_Os02g32630.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 93.381; most accessible tissue: Zhenshan97 young leaf, score: 96.065 |
vg0219342956 (J) | chr02 | 19342956 | C | A | 51.80% | 0.00% | A -> C | NA |
LOC_Os02g32620.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 93.412; most accessible tissue: Zhenshan97 flag leaf, score: 96.074 |
vg0219342957 (J) | chr02 | 19342957 | A | G | 51.70% | 0.00% | G -> A | NA |
LOC_Os02g32620.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 93.410; most accessible tissue: Zhenshan97 flag leaf, score: 96.074 |
vg0219342960 (J) | chr02 | 19342960 | C | A | 82.00% | 0.00% | C -> A |
mr1063 (Ind_All); LR P-value: 9.13E-06;
mr1213 (Jap_All); LR P-value: 8.02E-06; mr1215 (Ind_All); LR P-value: 6.78E-06; mr1460 (Ind_All); LMM P-value: 2.52E-06; LR P-value: 2.52E-06; mr1215_2 (Ind_All); LR P-value: 7.46E-06; mr1220_2 (Ind_All); LR P-value: 6.05E-06; mr1381_2 (Ind_All); LR P-value: 8.64E-06; mr1661_2 (Ind_All); LR P-value: 5.10E-07; mr1696_2 (Ind_All); LR P-value: 3.65E-06 |
LOC_Os02g32620.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 93.463; most accessible tissue: Zhenshan97 flag leaf, score: 96.129 |
vg0219343200 (J) | chr02 | 19343200 | G | C | 65.30% | 0.38% | G -> C | NA |
LOC_Os02g32620.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g32620.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 93.616; most accessible tissue: Zhenshan97 flag leaf, score: 96.171 |
vg0219343219 (J) | chr02 | 19343219 | G | A | 81.50% | 1.23% | G -> A | NA |
LOC_Os02g32620.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g32620.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 93.900; most accessible tissue: Zhenshan97 root, score: 96.529 |
vg0219343316 (J) | chr02 | 19343316 | C | T | 97.50% | 0.59% | C -> T | NA |
LOC_Os02g32620.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g32620.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 94.719; most accessible tissue: Zhenshan97 root, score: 97.104 |
STR0219343193 (J) | chr02 | 19343193 | CGCCGCC G | CGCCGCC C | 47.80% | 0.00% | CGCCGCCG -> CGCCGCCC | NA |
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