45 variations found. Os12g0638100/LOC_Os12g44090 (leucine-rich repeat family protein; putative; expressed), ranging from 27,340,224 bp to 27,344,135 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os12g44090 | leucine-rich repeat family protein, putative, expressed; RAP ID: Os12g0638100; MSU ID: LOC_Os12g44090 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| STR1227340363 (J) | chr12 | 27340363 | AAGA | A | 98.20% | 0.00% | AAGA -> A | NA |
|
| STR1227343079 (J) | chr12 | 27343079 | CACACAC ACACA | CACACAC ACA | 65.00% | 0.00% | CACACACACA -> CACACACACA CA | NA |
|
| STR1227343849 (J) | chr12 | 27343849 | CATCCAT CC | CATCCAT CCATCCA TCC | 43.00% | 0.00% | CATCCATCCA TCC -> CATCCATCC, CATCCATCCA TCCATCC | NA |
|
| vg1227340227 (J) | chr12 | 27340227 | C | T | 66.60% | 0.00% | T -> C |
mr1024 (All); LR P-value: 4.39E-29;
mr1579 (All); LR P-value: 3.72E-12; mr1701 (All); LR P-value: 6.25E-13; mr1922 (All); LR P-value: 8.03E-32; mr1940 (All); LR P-value: 8.45E-12; mr1024_2 (All); LMM P-value: 9.37E-06; LR P-value: 8.31E-27; mr1162_2 (All); LR P-value: 7.75E-15; mr1657_2 (All); LR P-value: 5.82E-20; mr1891_2 (All); LR P-value: 1.03E-30; mr1922_2 (All); LR P-value: 1.41E-19 |
LOC_Os12g44090.1 Alt: C| splice_region_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os12g44090.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g44080.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 67.704; most accessible tissue: Callus, score: 95.672 |
| vg1227340278 (J) | chr12 | 27340278 | GA | G | 60.70% | 0.00% | G -> GA,GAA,GAA A | NA |
LOC_Os12g44090.1 Alt: GAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g44080.1 Alt: GAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g44090.1 Alt: GAAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g44080.1 Alt: GAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g44090.1 Alt: GA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g44080.1 Alt: GA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.535; most accessible tissue: Callus, score: 95.672 |
| vg1227340289 (J) | chr12 | 27340289 | A | G | 99.80% | 0.00% | A -> G | NA |
LOC_Os12g44090.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os12g44080.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 67.179; most accessible tissue: Callus, score: 95.672 |
| vg1227340362 (J) | chr12 | 27340362 | AAAG | A | 95.50% | 0.00% | AAAG -> A | NA |
LOC_Os12g44090.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g44080.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 71.091; most accessible tissue: Zhenshan97 panicle, score: 95.602 |
| vg1227340569 (J) | chr12 | 27340569 | C | A | 99.60% | 0.00% | C -> A | NA |
LOC_Os12g44090.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 75.300; most accessible tissue: Zhenshan97 panicle, score: 94.518 |
| vg1227340657 (J) | chr12 | 27340657 | G | A | 66.60% | 0.00% | A -> G |
mr1024 (All); LR P-value: 6.59E-29;
mr1579 (All); LR P-value: 3.64E-12; mr1701 (All); LR P-value: 6.23E-13; mr1922 (All); LR P-value: 1.42E-30; mr1940 (All); LR P-value: 6.25E-12; mr1024_2 (All); LMM P-value: 4.89E-06; LR P-value: 5.76E-27; mr1657_2 (All); LR P-value: 4.08E-20; mr1891_2 (All); LR P-value: 2.42E-30; mr1922_2 (All); LR P-value: 1.66E-19 |
LOC_Os12g44090.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 75.056; most accessible tissue: Zhenshan97 panicle, score: 94.518 |
| vg1227341118 (J) | chr12 | 27341118 | C | T | 95.50% | 0.00% | C -> T |
LOC_Os12g44080.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g44090.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 64.131; most accessible tissue: Zhenshan97 panicle, score: 93.244 |
|
| vg1227341379 (J) | chr12 | 27341379 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os12g44090.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os12g44080.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g44100.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 67.823; most accessible tissue: Zhenshan97 panicle, score: 94.360 |
| vg1227341466 (J) | chr12 | 27341466 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os12g44090.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os12g44080.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g44100.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 66.655; most accessible tissue: Zhenshan97 panicle, score: 92.270 |
| vg1227342230 (J) | chr12 | 27342230 | G | T | 75.30% | 0.00% | G -> T | NA |
LOC_Os12g44090.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 61.897; most accessible tissue: Zhenshan97 panicle, score: 84.374 |
| vg1227342298 (J) | chr12 | 27342298 | C | A | 66.70% | 0.00% | A -> C |
mr1024 (All); LR P-value: 3.84E-29;
mr1542 (All); LR P-value: 4.81E-35; mr1579 (All); LR P-value: 8.42E-13; mr1670 (All); LR P-value: 1.37E-34; mr1701 (All); LR P-value: 1.40E-13; mr1922 (All); LR P-value: 8.75E-32; mr1940 (All); LR P-value: 4.98E-12; mr1024_2 (All); LMM P-value: 6.15E-06; LR P-value: 4.72E-27; mr1162_2 (All); LR P-value: 5.55E-15; mr1657_2 (All); LR P-value: 3.92E-20; mr1891_2 (All); LR P-value: 1.88E-30; mr1922_2 (All); LR P-value: 7.01E-20 |
LOC_Os12g44080.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g44100.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g44090.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 59.338; most accessible tissue: Callus, score: 82.031 |
| vg1227342306 (J) | chr12 | 27342306 | A | G | 59.90% | 0.00% | G -> A |
mr1021 (All); LR P-value: 2.10E-20;
mr1551 (All); LR P-value: 3.62E-24; mr1721 (All); LR P-value: 4.25E-42; mr1793 (All); LR P-value: 4.94E-28; mr1916 (All); LR P-value: 5.16E-17; mr1943 (All); LR P-value: 2.15E-21; mr1323_2 (All); LR P-value: 7.93E-26; mr1325_2 (All); LR P-value: 1.41E-13; mr1326_2 (All); LR P-value: 9.33E-14; mr1551_2 (All); LR P-value: 1.82E-21; mr1671_2 (All); LR P-value: 1.66E-76; mr1721_2 (All); LR P-value: 1.95E-49; mr1744_2 (All); LR P-value: 5.63E-16; mr1916_2 (All); LR P-value: 2.47E-26 |
LOC_Os12g44080.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g44100.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g44090.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 58.907; most accessible tissue: Callus, score: 82.031 |
| vg1227342436 (J) | chr12 | 27342436 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os12g44090.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os12g44080.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g44100.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 51.743; most accessible tissue: Callus, score: 79.181 |
| vg1227342562 (J) | chr12 | 27342562 | G | A | 97.90% | 0.00% | G -> A | NA |
LOC_Os12g44080.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g44100.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g44090.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 50.346; most accessible tissue: Callus, score: 79.181 |
| vg1227342757 (J) | chr12 | 27342757 | A | G | 66.70% | 0.00% | G -> A |
LOC_Os12g44090.1 Alt: A| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os12g44080.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g44100.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 48.596; most accessible tissue: Zhenshan97 panicle, score: 79.799 |
|
| vg1227342895 (J) | chr12 | 27342895 | C | T | 97.70% | 0.00% | C -> T,A | NA |
LOC_Os12g44090.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os12g44100.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g44090.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 53.372; most accessible tissue: Zhenshan97 panicle, score: 82.888 |
| vg1227342909 (J) | chr12 | 27342909 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os12g44090.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os12g44100.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 51.211; most accessible tissue: Zhenshan97 panicle, score: 81.135 |
| vg1227343078 (J) | chr12 | 27343078 | GCA | G | 66.10% | 0.00% | G -> GCA | NA |
LOC_Os12g44090.1 Alt: GCA| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os12g44100.1 Alt: GCA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 60.430; most accessible tissue: Zhenshan97 panicle, score: 83.904 |
| vg1227343099 (J) | chr12 | 27343099 | A | G | 95.50% | 0.00% | A -> G |
LOC_Os12g44100.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g44090.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 60.494; most accessible tissue: Zhenshan97 panicle, score: 83.904 |
|
| vg1227343228 (J) | chr12 | 27343228 | G | A | 97.90% | 0.00% | G -> A | NA |
LOC_Os12g44090.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 61.844; most accessible tissue: Zhenshan97 panicle, score: 86.058 |
| vg1227343327 (J) | chr12 | 27343327 | G | T | 75.20% | 0.11% | G -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g44100.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g44090.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 60.584; most accessible tissue: Zhenshan97 panicle, score: 86.058 |
| vg1227343398 (J) | chr12 | 27343398 | C | T | 66.60% | 0.00% | T -> C |
LOC_Os12g44090.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 58.389; most accessible tissue: Zhenshan97 panicle, score: 87.126 |
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