8 variations found. Os09g0572600/LOC_Os09g39930 (tyrosine protein kinase domain containing protein; putative; expressed), ranging from 22,902,938 bp to 22,904,835 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os09g39930 | tyrosine protein kinase domain containing protein, putative, expressed; RAP ID: Os09g0572600; MSU ID: LOC_Os09g39930 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0922903600 (J) | chr09 | 22903600 | C | T | 61.70% | 0.28% | T -> C |
Awn_length (All); LR P-value: 3.62E-17;
mr1064 (All); LR P-value: 9.84E-39; mr1092 (All); LR P-value: 1.18E-43; mr1228 (All); LR P-value: 2.54E-15; mr1534 (All); LR P-value: 8.33E-43; mr1865 (All); LR P-value: 2.27E-71; mr1064_2 (All); LR P-value: 4.16E-60; mr1256_2 (All); LR P-value: 2.58E-33; mr1324_2 (All); LR P-value: 1.31E-14; mr1325_2 (All); LR P-value: 2.85E-12; mr1386_2 (All); LR P-value: 7.77E-23; mr1623_2 (All); LR P-value: 3.67E-07 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g39930.1 Alt: C| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os09g39940.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g39920.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0922903611 (J) | chr09 | 22903611 | T | TTACCGG CA | 99.50% | 0.00% | T -> TTACCGGCA | NA |
LOC_Os09g39930.1 Alt: TTACCGGCA| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0922903788 (J) | chr09 | 22903788 | T | G | 61.60% | 0.04% | G -> T |
Awn_length (All); LR P-value: 3.62E-17;
mr1064 (All); LR P-value: 9.84E-39; mr1092 (All); LR P-value: 1.18E-43; mr1228 (All); LR P-value: 2.54E-15; mr1534 (All); LR P-value: 8.33E-43; mr1865 (All); LR P-value: 2.27E-71; mr1064_2 (All); LR P-value: 4.16E-60; mr1256_2 (All); LR P-value: 2.58E-33; mr1324_2 (All); LR P-value: 1.31E-14; mr1325_2 (All); LR P-value: 2.85E-12; mr1386_2 (All); LR P-value: 7.77E-23; mr1623_2 (All); LR P-value: 3.67E-07 |
LOC_Os09g39930.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g39930.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0922904079 (J) | chr09 | 22904079 | T | A | 61.70% | 0.00% | A -> T |
mr1064 (All); LR P-value: 3.54E-37;
mr1092 (All); LR P-value: 1.65E-44; mr1228 (All); LR P-value: 3.74E-16; mr1534 (All); LR P-value: 1.62E-40; mr1865 (All); LR P-value: 5.90E-70; mr1064_2 (All); LR P-value: 6.53E-58; mr1081_2 (All); LR P-value: 2.30E-32; mr1256_2 (All); LR P-value: 1.17E-34; mr1325_2 (All); LR P-value: 2.16E-12; mr1386_2 (All); LR P-value: 1.52E-23 |
LOC_Os09g39930.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0922904550 (J) | chr09 | 22904550 | A | G | 61.60% | 0.00% | G -> A |
LOC_Os09g39930.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
|
| vg0922904665 (J) | chr09 | 22904665 | GTC | GTCTC | 96.70% | 0.00% | GTC -> GTCTC,G,GT CTCTC | NA |
LOC_Os09g39930.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g39940.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g39950.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g39920.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g39930.1 Alt: GTCTC| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g39940.1 Alt: GTCTC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g39950.1 Alt: GTCTC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g39920.1 Alt: GTCTC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g39930.1 Alt: GTCTCTC| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g39940.1 Alt: GTCTCTC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g39950.1 Alt: GTCTCTC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g39920.1 Alt: GTCTCTC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0922904756 (J) | chr09 | 22904756 | C | T | 58.70% | 0.34% | T -> C |
mr1063 (All); LR P-value: 7.36E-48;
mr1064 (All); LR P-value: 2.84E-37; mr1088 (All); LR P-value: 2.39E-58; mr1125 (All); LR P-value: 1.80E-49; mr1164 (All); LR P-value: 3.11E-15; mr1246 (All); LR P-value: 5.72E-62; mr1404 (All); LR P-value: 3.02E-34; mr1426 (All); LR P-value: 6.69E-29; mr1534 (All); LR P-value: 4.13E-41; mr1591 (All); LR P-value: 4.31E-42; mr1655 (All); LR P-value: 9.41E-13; mr1721 (All); LR P-value: 1.38E-39; mr1865 (All); LMM P-value: 1.13E-06; mr1970 (All); LR P-value: 1.63E-63; mr1973 (All); LR P-value: 7.06E-80; mr1064_2 (All); LR P-value: 6.90E-58; mr1125_2 (All); LR P-value: 7.04E-64; mr1164_2 (All); LR P-value: 1.17E-20; mr1208_2 (All); LR P-value: 2.45E-38; mr1323_2 (All); LR P-value: 1.57E-26; mr1744_2 (All); LR P-value: 2.95E-15; mr1745_2 (All); LR P-value: 4.04E-39; mr1782_2 (All); LR P-value: 8.98E-10; mr1922_2 (All); LR P-value: 1.50E-19; mr1970_2 (All); LR P-value: 9.27E-63 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g39930.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g39940.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g39950.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g39920.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| STR0922904755 (J) | chr09 | 22904755 | GC | GT | 60.90% | 0.00% | GT -> GC | NA |
|