21 variations found. Os05g0491400/LOC_Os05g41230 (BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1 precursor; putative; expressed), ranging from 24,149,268 bp to 24,151,542 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os05g41230 | BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1 precursor, putative, expressed; RAP ID: Os05g0491400; MSU ID: LOC_Os05g41230 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0524149359 (J) | chr05 | 24149359 | TACTATG CCAGTA | T | 97.40% | 0.00% | TACTATGCCA GTA -> T | NA |
LOC_Os05g41230.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g41240.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41240.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41240.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.366; most accessible tissue: Minghui63 panicle, score: 87.951 |
| vg0524149426 (J) | chr05 | 24149426 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os05g41230.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os05g41240.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g41240.3 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g41240.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 75.500; most accessible tissue: Callus, score: 91.991 |
| vg0524149523 (J) | chr05 | 24149523 | C | A | 99.30% | 0.00% | C -> A | NA |
LOC_Os05g41230.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g41240.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41240.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41240.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.064; most accessible tissue: Callus, score: 91.991 |
| vg0524149624 (J) | chr05 | 24149624 | C | T | 52.30% | 0.30% | C -> T | NA |
LOC_Os05g41230.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os05g41230.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 73.203; most accessible tissue: Zhenshan97 panicle, score: 86.432 |
| vg0524149702 (J) | chr05 | 24149702 | T | C | 97.50% | 0.00% | T -> C | NA |
LOC_Os05g41240.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g41240.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41240.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41230.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.012; most accessible tissue: Minghui63 panicle, score: 90.408 |
| vg0524149804 (J) | chr05 | 24149804 | T | G | 49.90% | 0.28% | G -> T | NA |
LOC_Os05g41240.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g41240.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41240.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41230.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 75.857; most accessible tissue: Minghui63 panicle, score: 89.444 |
| vg0524149902 (J) | chr05 | 24149902 | GC | G | 99.80% | 0.00% | GC -> G | NA |
LOC_Os05g41230.1 Alt: G| frameshift_variant HIGH(snpEff)
LOC_Os05g41240.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g41240.3 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 71.246; most accessible tissue: Minghui63 panicle, score: 87.951 |
| vg0524150114 (J) | chr05 | 24150114 | A | G | 98.90% | 0.00% | A -> G | NA |
LOC_Os05g41230.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os05g41240.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g41240.3 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g41240.2 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 71.128; most accessible tissue: Minghui63 panicle, score: 86.850 |
| vg0524150176 (J) | chr05 | 24150176 | A | G | 49.90% | 0.25% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g41240.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41240.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41240.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41230.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 71.287; most accessible tissue: Callus, score: 94.373 |
| vg0524150306 (J) | chr05 | 24150306 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os05g41240.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os05g41240.3 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g41240.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g41230.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 75.138; most accessible tissue: Callus, score: 94.373 |
| vg0524150375 (J) | chr05 | 24150375 | G | C | 55.70% | 0.00% | G -> C | NA |
LOC_Os05g41230.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 73.512; most accessible tissue: Minghui63 flower, score: 86.025 |
| vg0524150401 (J) | chr05 | 24150401 | G | T | 99.00% | 0.00% | G -> T | NA |
LOC_Os05g41230.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 75.213; most accessible tissue: Minghui63 flower, score: 87.009 |
| vg0524150557 (J) | chr05 | 24150557 | T | TCAAA | 33.70% | 0.00% | T -> TCAAA,TA,T CAA,TC,TCA AAA,TCAAAA A | NA |
LOC_Os05g41240.1 Alt: TCAAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g41240.3 Alt: TCAAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41240.2 Alt: TCAAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41230.1 Alt: TCAAAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41240.1 Alt: TCAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41240.3 Alt: TCAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41240.2 Alt: TCAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41230.1 Alt: TCAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41240.1 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41240.3 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41240.2 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41230.1 Alt: TA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41240.1 Alt: TCAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41240.3 Alt: TCAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41240.2 Alt: TCAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41230.1 Alt: TCAAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41240.1 Alt: TCAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41240.3 Alt: TCAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41240.2 Alt: TCAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41230.1 Alt: TCAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41240.1 Alt: TC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41240.3 Alt: TC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41240.2 Alt: TC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41230.1 Alt: TC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 72.029; most accessible tissue: Callus, score: 93.693 |
| vg0524150558 (J) | chr05 | 24150558 | A | C | 39.70% | 46.89% | A -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g41240.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41240.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41240.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41230.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 72.512; most accessible tissue: Callus, score: 93.693 |
| vg0524150578 (J) | chr05 | 24150578 | T | G | 50.00% | 0.21% | T -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g41240.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41240.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41240.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41230.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 71.253; most accessible tissue: Minghui63 flower, score: 85.573 |
| vg0524150679 (J) | chr05 | 24150679 | C | CA | 49.70% | 0.28% | CA -> C,CAA | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g41240.1 Alt: CAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41240.3 Alt: CAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41240.2 Alt: CAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41230.1 Alt: CAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41240.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41240.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41240.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41230.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 69.975; most accessible tissue: Callus, score: 97.584 |
| vg0524150786 (J) | chr05 | 24150786 | C | T | 94.20% | 0.00% | C -> T |
mr1612 (All); LR P-value: 1.52E-13;
mr1989 (All); LR P-value: 6.70E-09; mr1119_2 (All); LR P-value: 4.41E-17; mr1120_2 (All); LR P-value: 2.40E-21; mr1126_2 (All); LR P-value: 5.91E-09; mr1166_2 (All); LR P-value: 3.52E-12; mr1567_2 (All); LR P-value: 8.81E-09; mr1612_2 (All); LR P-value: 2.10E-13; mr1765_2 (All); LR P-value: 5.92E-09 |
LOC_Os05g41230.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 88.098; most accessible tissue: Callus, score: 97.584 |
| vg0524151064 (J) | chr05 | 24151064 | C | CA | 50.20% | 0.00% | CA -> C | NA |
LOC_Os05g41240.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g41240.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41240.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41230.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 94.080; most accessible tissue: Callus, score: 98.480 |
| vg0524151079 (J) | chr05 | 24151079 | G | A | 86.60% | 0.00% | A -> G |
Heading_date (All); LR P-value: 3.34E-10;
Plant_height (Jap_All); LR P-value: 2.65E-18; Spikelet_length (All); LR P-value: 1.81E-16; Spikelet_length (Jap_All); LR P-value: 3.60E-13; mr1010 (All); LR P-value: 2.21E-13; mr1010 (Jap_All); LR P-value: 6.29E-07; mr1026 (Jap_All); LR P-value: 6.81E-06; mr1031 (All); LR P-value: 1.94E-12; mr1045 (All); LR P-value: 1.15E-08; mr1045 (Jap_All); LR P-value: 5.57E-06; mr1056 (All); LR P-value: 6.14E-13; mr1063 (Jap_All); LR P-value: 4.28E-06; mr1069 (Jap_All); LR P-value: 1.84E-06; mr1077 (Jap_All); LR P-value: 1.10E-07; mr1115 (All); LR P-value: 7.05E-24; mr1137 (All); LR P-value: 5.19E-31; mr1137 (Jap_All); LR P-value: 3.40E-10; mr1161 (Jap_All); LR P-value: 3.91E-06; mr1163 (All); LR P-value: 5.85E-22; mr1163 (Jap_All); LR P-value: 2.29E-07; mr1164 (Jap_All); LR P-value: 6.87E-07; mr1180 (Jap_All); LR P-value: 2.69E-06; mr1183 (Jap_All); LR P-value: 1.88E-08; mr1202 (Jap_All); LR P-value: 9.40E-08; mr1206 (Jap_All); LR P-value: 2.84E-07; mr1252 (All); LR P-value: 4.03E-09; mr1252 (Jap_All); LR P-value: 1.10E-07; mr1330 (Jap_All); LR P-value: 2.82E-07; mr1486 (Jap_All); LR P-value: 1.36E-10; mr1503 (Jap_All); LR P-value: 7.85E-08; mr1521 (Jap_All); LR P-value: 6.19E-08; mr1530 (Jap_All); LR P-value: 3.35E-06; mr1548 (Jap_All); LR P-value: 1.29E-07; mr1576 (All); LR P-value: 5.43E-07; mr1611 (All); LR P-value: 1.20E-23; mr1617 (All); LR P-value: 3.82E-26; mr1617 (Jap_All); LR P-value: 2.53E-08; mr1626 (All); LR P-value: 2.50E-11; mr1627 (Jap_All); LR P-value: 4.91E-08; mr1668 (Jap_All); LR P-value: 1.28E-08; mr1712 (All); LR P-value: 6.60E-10; mr1748 (All); LR P-value: 1.42E-07; mr1763 (All); LR P-value: 7.41E-08; mr1763 (Jap_All); LR P-value: 6.96E-06; mr1775 (Jap_All); LR P-value: 3.53E-06; mr1824 (Jap_All); LMM P-value: 4.23E-06; LR P-value: 4.22E-06; mr1880 (All); LR P-value: 7.26E-07; mr1920 (All); LR P-value: 9.70E-23; mr1977 (All); LR P-value: 1.73E-08; mr1977 (Jap_All); LR P-value: 2.96E-06; mr1002_2 (All); LR P-value: 8.01E-10; mr1010_2 (All); LR P-value: 1.13E-21; mr1010_2 (Jap_All); LR P-value: 5.38E-09; mr1011_2 (All); LR P-value: 4.38E-12; mr1011_2 (Jap_All); LR P-value: 1.75E-07; mr1045_2 (All); LR P-value: 4.71E-07; mr1051_2 (Jap_All); LR P-value: 8.21E-07; mr1072_2 (Jap_All); LR P-value: 7.44E-06; mr1077_2 (Jap_All); LR P-value: 4.68E-06; mr1137_2 (Jap_All); LR P-value: 2.17E-09; mr1164_2 (Jap_All); LR P-value: 5.78E-07; mr1182_2 (All); LR P-value: 4.64E-13; mr1182_2 (Jap_All); LR P-value: 5.33E-06; mr1229_2 (All); LR P-value: 1.24E-06; mr1252_2 (All); LR P-value: 5.04E-07; mr1330_2 (Jap_All); LR P-value: 1.03E-07; mr1359_2 (Jap_All); LR P-value: 2.92E-07; mr1441_2 (Jap_All); LR P-value: 4.59E-07; mr1486_2 (Jap_All); LR P-value: 6.00E-11; mr1530_2 (Jap_All); LR P-value: 1.22E-10; mr1555_2 (All); LR P-value: 1.13E-07; mr1576_2 (All); LR P-value: 2.30E-09; mr1576_2 (Jap_All); LR P-value: 4.53E-06; mr1588_2 (Jap_All); LR P-value: 3.47E-06; mr1617_2 (Jap_All); LR P-value: 9.72E-07; mr1627_2 (Jap_All); LR P-value: 5.84E-06; mr1671_2 (Jap_All); LR P-value: 1.45E-07; mr1709_2 (Jap_All); LR P-value: 1.31E-09; mr1748_2 (All); LR P-value: 2.65E-08; mr1805_2 (Jap_All); LR P-value: 1.02E-08; mr1825_2 (Jap_All); LR P-value: 1.14E-09; mr1880_2 (All); LR P-value: 2.27E-08; mr1880_2 (Jap_All); LR P-value: 2.27E-07; mr1957_2 (All); LR P-value: 9.15E-06 |
LOC_Os05g41240.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g41240.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41240.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g41230.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 93.518; most accessible tissue: Minghui63 young leaf, score: 95.163 |
| vg0524151377 (J) | chr05 | 24151377 | G | A | 96.70% | 0.00% | G -> A |
LOC_Os05g41230.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 83.151; most accessible tissue: Minghui63 panicle, score: 90.184 |
|
| STR0524151065 (J) | chr05 | 24151065 | AA | A | 49.60% | 0.00% | AA -> A | NA |
|