18 variations found. Os03g0120900/LOC_Os03g02900 (B3 DNA binding domain containing protein; expressed), ranging from 1,152,917 bp to 1,154,876 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os03g02900 | B3 DNA binding domain containing protein, expressed; RAP ID: Os03g0120900; MSU ID: LOC_Os03g02900 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0301153013 (J) | chr03 | 1153013 | GCACACA | GCA | 54.30% | 0.00% | GCA -> GCACACA,GC ACA,GCACAC ACA,G,GCAC ACACACACA | NA |
LOC_Os03g02900.1 Alt: GCACA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g02900.1 Alt: GCACACA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g02900.1 Alt: GCACACACACACA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g02900.1 Alt: GCACACACA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g02900.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0301153121 (J) | chr03 | 1153121 | G | T | 84.90% | 0.00% | T -> G |
mr1002 (All); LR P-value: 5.49E-09;
mr1002 (Jap_All); LR P-value: 1.02E-06; mr1182 (All); LR P-value: 3.04E-11; mr1790 (All); LR P-value: 1.14E-09; mr1805 (Jap_All); LR P-value: 4.67E-07; mr1002_2 (All); LR P-value: 2.23E-11; mr1002_2 (Jap_All); LR P-value: 1.17E-08; mr1010_2 (Jap_All); LR P-value: 1.72E-07; mr1020_2 (All); LR P-value: 2.86E-06; mr1164_2 (Jap_All); LR P-value: 4.62E-06; mr1182_2 (All); LR P-value: 1.35E-12; mr1330_2 (Jap_All); LR P-value: 5.09E-06; mr1576_2 (All); LR P-value: 5.02E-10 |
LOC_Os03g02900.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0301153253 (J) | chr03 | 1153253 | G | A | 64.70% | 0.00% | A -> G |
LOC_Os03g02900.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
|
| vg0301153719 (J) | chr03 | 1153719 | C | A | 60.40% | 0.00% | A -> C |
LOC_Os03g02900.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
|
| vg0301153822 (J) | chr03 | 1153822 | C | G | 99.80% | 0.00% | C -> G | NA |
LOC_Os03g02900.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0301153905 (J) | chr03 | 1153905 | A | AGCCGCC GCC | 57.90% | 0.00% | AGCCGCCGCC -> A,AGCC | NA |
LOC_Os03g02900.1 Alt: A| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os03g02900.1 Alt: AGCC| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0301153922 (J) | chr03 | 1153922 | CCGCCGC CGCCGG | C | 99.80% | 0.00% | CCGCCGCCGC CGG -> C | NA |
LOC_Os03g02900.1 Alt: C| inframe_deletion MODERATE(snpEff)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0301153934 (J) | chr03 | 1153934 | G | C | 79.10% | 0.00% | G -> C,GCCGCCGC CGC |
mr1249 (All); LR P-value: 7.79E-08;
mr1559 (All); LR P-value: 1.67E-07; mr1002_2 (Jap_All); LR P-value: 8.39E-09; mr1092_2 (Jap_All); LR P-value: 3.31E-06; mr1152_2 (Jap_All); LR P-value: 6.91E-06; mr1154_2 (Jap_All); LR P-value: 1.44E-06; mr1164_2 (All); LR P-value: 6.55E-21; mr1164_2 (Jap_All); LR P-value: 2.40E-07; mr1263_2 (All); LR P-value: 4.30E-06; mr1359_2 (Jap_All); LR P-value: 2.55E-06; mr1548_2 (All); LR P-value: 1.38E-07 |
LOC_Os03g02900.1 Alt: C/nonsynonymous_codon(CooVar)
LOC_Os03g02900.1 Alt: GCCGCCGCCGC| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0301153982 (J) | chr03 | 1153982 | A | G | 99.90% | 0.00% | A -> G | NA |
LOC_Os03g02900.1 Alt: G| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0301154094 (J) | chr03 | 1154094 | T | G | 60.20% | 0.00% | G -> T |
LOC_Os03g02900.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
|
| vg0301154224 (J) | chr03 | 1154224 | A | G | 60.30% | 0.00% | G -> A |
LOC_Os03g02900.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
|
| vg0301154415 (J) | chr03 | 1154415 | G | A | 84.80% | 0.00% | A -> G |
mr1002 (All); LR P-value: 4.78E-09;
mr1002 (Jap_All); LR P-value: 6.77E-07; mr1182 (All); LR P-value: 3.43E-11; mr1790 (All); LR P-value: 1.19E-09; mr1805 (Jap_All); LR P-value: 6.42E-07; mr1002_2 (All); LR P-value: 2.30E-11; mr1002_2 (Jap_All); LR P-value: 1.30E-08; mr1010_2 (Jap_All); LR P-value: 5.35E-08; mr1020_2 (All); LR P-value: 3.00E-06; mr1164_2 (Jap_All); LR P-value: 4.62E-06; mr1182_2 (All); LR P-value: 1.29E-12; mr1330_2 (Jap_All); LR P-value: 5.28E-06; mr1576_2 (All); LR P-value: 4.91E-10 |
LOC_Os03g02900.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0301154447 (J) | chr03 | 1154447 | T | C | 60.40% | 0.00% | C -> T |
Yield (All); LR P-value: 6.76E-19;
mr1020_2 (All); LR P-value: 2.10E-06; mr1024_2 (All); LR P-value: 4.11E-25; mr1349_2 (All); LR P-value: 7.66E-10; mr1401_2 (All); LR P-value: 1.10E-21; mr1567_2 (Ind_All); LR P-value: 2.01E-07; mr1666_2 (All); LR P-value: 7.10E-13; mr1728_2 (All); LR P-value: 6.56E-11; mr1835_2 (All); LR P-value: 5.20E-09; mr1940_2 (All); LR P-value: 1.85E-08 |
LOC_Os03g02900.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0301154581 (J) | chr03 | 1154581 | A | G | 60.30% | 0.21% | G -> A |
LOC_Os03g02900.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
|
| vg0301154594 (J) | chr03 | 1154594 | AC | A | 60.30% | 0.00% | A -> AC | NA |
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
|
| vg0301154652 (J) | chr03 | 1154652 | C | T | 98.10% | 0.00% | C -> T | NA |
LOC_Os03g02900.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0301154823 (J) | chr03 | 1154823 | T | A | 99.00% | 0.00% | T -> A | NA |
LOC_Os03g02900.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| STR0301154598 (J) | chr03 | 1154598 | AAA | AA | 61.10% | 0.00% | AA -> AAA | NA |
|