16 variations found. LOC_Os03g24930 (tyrosine protein kinase domain containing protein; putative; expressed), ranging from 14,206,980 bp to 14,209,164 bp (including 0 kb upstream and 0 kb downstream of the gene).
| 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 |
|---|---|---|---|---|---|---|---|---|---|
| STR0314209147 (J) | chr03 | 14209147 | TTT | TTTT | 52.70% | 0.00% | TT -> TTT,TTTT | NA |
|
| vg0314207141 (J) | chr03 | 14207141 | A | T | 86.90% | 0.00% | A -> T | NA |
LOC_Os03g24930.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g24930.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 94.428; most accessible tissue: Minghui63 root, score: 98.486 |
| vg0314207222 (J) | chr03 | 14207222 | C | G | 96.90% | 0.00% | C -> G | NA |
LOC_Os03g24930.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 94.119; most accessible tissue: Minghui63 flag leaf, score: 97.753 |
| vg0314207262 (J) | chr03 | 14207262 | C | G | 87.10% | 0.00% | C -> G | NA |
LOC_Os03g24930.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 93.288; most accessible tissue: Minghui63 flag leaf, score: 97.701 |
| vg0314207416 (J) | chr03 | 14207416 | G | T | 98.10% | 0.00% | G -> T | NA |
LOC_Os03g24930.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 86.598; most accessible tissue: Minghui63 flag leaf, score: 97.113 |
| vg0314207421 (J) | chr03 | 14207421 | T | C | 99.40% | 0.00% | T -> C | NA |
LOC_Os03g24930.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 86.655; most accessible tissue: Minghui63 flag leaf, score: 97.173 |
| vg0314207642 (J) | chr03 | 14207642 | T | G | 99.90% | 0.00% | T -> G | NA |
LOC_Os03g24930.1 Alt: G| splice_donor_variant&intron_variant HIGH(snpEff)
The average chromatin accessibility score: 85.852; most accessible tissue: Minghui63 flag leaf, score: 96.597 |
| vg0314207681 (J) | chr03 | 14207681 | G | C | 99.90% | 0.00% | G -> C | NA |
LOC_Os03g24930.2 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os03g24930.1 Alt: C| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 85.278; most accessible tissue: Minghui63 flag leaf, score: 96.434 |
| vg0314207934 (J) | chr03 | 14207934 | GCGCCGC CGCCGC | GCGC | 54.40% | 0.00% | GCGCCGCCGC CGC -> GCGC,GCGCC GCCGCCGCCG CCGC,G | NA |
LOC_Os03g24930.1 Alt: GCGC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g24930.2 Alt: GCGC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g24930.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g24930.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g24930.1 Alt: GCGCCGCCGCCGCCGCCGC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g24930.2 Alt: GCGCCGCCGCCGCCGCCGC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 84.378; most accessible tissue: Minghui63 flag leaf, score: 97.221 |
| vg0314208267 (J) | chr03 | 14208267 | G | T | 64.20% | 0.00% | T -> G |
LOC_Os03g24930.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g24930.2 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 87.944; most accessible tissue: Minghui63 flag leaf, score: 98.473 |
|
| vg0314208411 (J) | chr03 | 14208411 | C | T | 62.40% | 0.00% | T -> C |
mr1027 (All); LR P-value: 1.09E-65;
mr1064 (All); LR P-value: 5.07E-38; mr1072 (All); LR P-value: 2.32E-26; mr1075 (All); LR P-value: 3.97E-30; mr1077 (All); LR P-value: 1.53E-18; mr1124 (All); LR P-value: 1.66E-39; mr1309 (All); LR P-value: 5.72E-27; mr1517 (All); LR P-value: 1.53E-86; mr1534 (All); LR P-value: 1.01E-39; mr1538 (All); LR P-value: 1.53E-66; mr1563 (All); LR P-value: 3.68E-45; mr1566 (All); LR P-value: 6.64E-19; mr1594 (All); LR P-value: 1.78E-57; mr1595 (All); LR P-value: 2.61E-08; mr1629 (All); LR P-value: 3.49E-77; mr1737 (All); LR P-value: 7.34E-30; mr1795 (All); LR P-value: 5.51E-55; mr1861 (All); LR P-value: 3.59E-54; mr1890 (All); LR P-value: 1.36E-38; mr1962 (All); LR P-value: 1.31E-58; mr1081_2 (All); LR P-value: 5.12E-32; mr1124_2 (All); LR P-value: 3.63E-54; mr1256_2 (All); LR P-value: 5.60E-33; mr1386_2 (All); LR P-value: 1.05E-23; mr1841_2 (All); LR P-value: 9.70E-32 |
LOC_Os03g24930.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g24930.2 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 86.192; most accessible tissue: Minghui63 flag leaf, score: 98.394 |
| vg0314208697 (J) | chr03 | 14208697 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os03g24930.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os03g24930.2 Alt: A| missense_variant MODERATE(snpEff) LOC_Os03g24940.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g24940.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 91.533; most accessible tissue: Minghui63 flag leaf, score: 98.522 |
| vg0314208722 (J) | chr03 | 14208722 | A | T | 99.30% | 0.00% | A -> T | NA |
LOC_Os03g24930.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os03g24930.2 Alt: T| missense_variant MODERATE(snpEff) LOC_Os03g24940.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g24940.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 91.623; most accessible tissue: Minghui63 flag leaf, score: 98.532 |
| vg0314208825 (J) | chr03 | 14208825 | GC | G | 86.90% | 0.00% | GC -> G,AC | NA |
LOC_Os03g24930.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g24930.2 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g24940.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g24940.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g24930.1 Alt: AC| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g24930.2 Alt: AC| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g24940.1 Alt: AC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g24940.2 Alt: AC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 90.727; most accessible tissue: Minghui63 flag leaf, score: 98.345 |
| vg0314208943 (J) | chr03 | 14208943 | AT | A | 51.10% | 0.00% | AT -> A | NA |
LOC_Os03g24930.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g24930.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g24940.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g24940.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 89.117; most accessible tissue: Minghui63 flag leaf, score: 97.957 |
| vg0314209146 (J) | chr03 | 14209146 | CT | C | 58.80% | 0.00% | C -> CT,CTT | NA |
LOC_Os03g24930.1 Alt: CTT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g24930.2 Alt: CTT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g24940.1 Alt: CTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g24940.2 Alt: CTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g24930.1 Alt: CT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g24930.2 Alt: CT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g24940.1 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g24940.2 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 71.736; most accessible tissue: Minghui63 flag leaf, score: 94.503 |
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