48 variations found. LOC_Os09g15840 (NBS-LRR disease resistance protein; putative; expressed), ranging from 9,673,999 bp to 9,674,695 bp (including 0 kb upstream and 0 kb downstream of the gene).
Rice quantitative trait nucleotides (QTNs) and inferred QTN effects are from Wei et al., Nature Genetics, 2021.
| Category | Variant ID | Chrom | Pos | Gene | MSU | RAP | Alt_Allele_Function | Ref_geno | Alt_geno |
|---|---|---|---|---|---|---|---|---|---|
| Biotic Stress | vg0909672381 | Chr9 | 9672381 | Pii/HIT7/pi5-1 | LOC_Os09g15840 | Os09g0327600 | increasing blast resistance | A | G |
| Biotic Stress | Chr9 | <MNP> | Pii/HIT7/pi5-1 | LOC_Os09g15840 | Os09g0327600 | increasing blast resistance | Ref | <MNP> |
| 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0909674007 (J) | chr09 | 9674007 | A | G | 72.70% | 23.15% | A -> G | NA |
LOC_Os09g15840.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 37.841; most accessible tissue: Zhenshan97 flower, score: 91.322 |
| vg0909674009 (J) | chr09 | 9674009 | T | A | 75.80% | 19.74% | T -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g15840.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 37.841; most accessible tissue: Zhenshan97 flower, score: 91.322 |
| vg0909674074 (J) | chr09 | 9674074 | T | A | 72.60% | 23.25% | T -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g15840.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 37.940; most accessible tissue: Zhenshan97 flower, score: 91.289 |
| vg0909674090 (J) | chr09 | 9674090 | T | A | 74.20% | 24.95% | T -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g15840.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 37.490; most accessible tissue: Zhenshan97 flower, score: 91.257 |
| vg0909674097 (J) | chr09 | 9674097 | CT | C | 72.80% | 23.49% | CT -> C,CAAT | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g15840.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g15840.1 Alt: CAAT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 37.684; most accessible tissue: Zhenshan97 flower, score: 91.289 |
| vg0909674099 (J) | chr09 | 9674099 | T | A | 72.80% | 23.28% | T -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g15840.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 37.873; most accessible tissue: Zhenshan97 flower, score: 91.483 |
| vg0909674103 (J) | chr09 | 9674103 | A | ACTGCAC | 73.00% | 23.61% | A -> ACTGCAC | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g15840.1 Alt: ACTGCAC| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 46.331; most accessible tissue: Zhenshan97 flower, score: 91.731 |
| vg0909674106 (J) | chr09 | 9674106 | A | AGTGGGT TGTAACT ATAT | 72.80% | 23.42% | A -> AGTGGGTTGT AACTATAT | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g15840.1 Alt: AGTGGGTTGTAACTATAT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 46.331; most accessible tissue: Zhenshan97 flower, score: 91.731 |
| vg0909674145 (J) | chr09 | 9674145 | A | T | 72.90% | 23.53% | A -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g15840.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 58.643; most accessible tissue: Zhenshan97 flower, score: 93.052 |
| vg0909674154 (J) | chr09 | 9674154 | A | C | 72.80% | 24.55% | A -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g15840.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 67.386; most accessible tissue: Zhenshan97 flower, score: 93.614 |
| vg0909674161 (J) | chr09 | 9674161 | A | ATTCTAG AC | 72.80% | 24.42% | A -> ATTCTAGAC | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g15840.1 Alt: ATTCTAGAC| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.305; most accessible tissue: Zhenshan97 flower, score: 93.695 |
| vg0909674175 (J) | chr09 | 9674175 | A | C | 72.50% | 24.48% | A -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g15840.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 70.163; most accessible tissue: Zhenshan97 flower, score: 93.634 |
| vg0909674220 (J) | chr09 | 9674220 | C | T | 74.10% | 24.46% | C -> T | NA |
LOC_Os09g15840.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g15840.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 80.180; most accessible tissue: Zhenshan97 flower, score: 94.812 |
| vg0909674221 (J) | chr09 | 9674221 | G | T | 72.80% | 23.97% | G -> T | NA |
LOC_Os09g15840.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g15840.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os09g15840.1 Alt: T| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 80.228; most accessible tissue: Zhenshan97 flower, score: 94.812 |
| vg0909674267 (J) | chr09 | 9674267 | A | AG | 72.70% | 24.80% | A -> AG | NA |
LOC_Os09g15840.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g15840.1 Alt: AG/frameshift_variant(CooVar) The average chromatin accessibility score: 83.678; most accessible tissue: Zhenshan97 flower, score: 95.260 |
| vg0909674298 (J) | chr09 | 9674298 | A | G | 74.40% | 24.57% | A -> G | NA |
LOC_Os09g15840.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os09g15840.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 86.556; most accessible tissue: Zhenshan97 flower, score: 95.222 |
| vg0909674309 (J) | chr09 | 9674309 | A | T | 73.30% | 0.00% | A -> T | NA |
LOC_Os09g15840.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 86.866; most accessible tissue: Zhenshan97 flower, score: 95.196 |
| vg0909674372 (J) | chr09 | 9674372 | G | A | 76.00% | 0.04% | G -> A | NA |
LOC_Os09g15840.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g15840.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 87.485; most accessible tissue: Zhenshan97 flower, score: 94.586 |
| vg0909674399 (J) | chr09 | 9674399 | G | A | 76.00% | 0.08% | G -> A | NA |
LOC_Os09g15840.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g15840.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 87.443; most accessible tissue: Minghui63 panicle, score: 94.638 |
| vg0909674401 (J) | chr09 | 9674401 | G | T | 99.40% | 0.00% | G -> T | NA |
LOC_Os09g15840.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 87.460; most accessible tissue: Minghui63 panicle, score: 94.638 |
| vg0909674408 (J) | chr09 | 9674408 | T | G | 77.40% | 0.06% | T -> G | NA |
LOC_Os09g15840.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os09g15840.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 87.517; most accessible tissue: Minghui63 panicle, score: 94.638 |
| vg0909674441 (J) | chr09 | 9674441 | G | A | 76.20% | 0.06% | G -> A | NA |
LOC_Os09g15840.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g15840.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 91.613; most accessible tissue: Minghui63 panicle, score: 95.645 |
| vg0909674447 (J) | chr09 | 9674447 | G | C | 70.90% | 0.11% | G -> C,A | NA |
LOC_Os09g15840.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g15840.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os09g15840.1 Alt: C| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar) LOC_Os09g15840.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 91.731; most accessible tissue: Minghui63 panicle, score: 95.645 |
| vg0909674448 (J) | chr09 | 9674448 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os09g15840.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 91.735; most accessible tissue: Minghui63 panicle, score: 95.645 |
| vg0909674450 (J) | chr09 | 9674450 | G | A | 76.20% | 0.06% | G -> A | NA |
LOC_Os09g15840.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g15840.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 91.793; most accessible tissue: Minghui63 panicle, score: 95.645 |
| vg0909674459 (J) | chr09 | 9674459 | A | C | 76.20% | 0.06% | A -> C | NA |
LOC_Os09g15840.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g15840.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 91.981; most accessible tissue: Minghui63 panicle, score: 95.645 |
| vg0909674461 (J) | chr09 | 9674461 | G | A | 76.20% | 0.06% | G -> A | NA |
LOC_Os09g15840.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g15840.1 Alt: A| missense_variant MODERATE(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 91.916; most accessible tissue: Minghui63 panicle, score: 95.645 |
| vg0909674477 (J) | chr09 | 9674477 | C | A | 73.20% | 0.13% | C -> A | NA |
LOC_Os09g15840.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g15840.1 Alt: A| missense_variant MODERATE(snpEff)/synonymous_codon(CooVar) LOC_Os09g15840.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 92.415; most accessible tissue: Minghui63 panicle, score: 95.645 |
| vg0909674479 (J) | chr09 | 9674479 | A | G | 71.10% | 0.11% | A -> G | NA |
LOC_Os09g15840.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os09g15840.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 92.505; most accessible tissue: Minghui63 panicle, score: 95.645 |
| vg0909674493 (J) | chr09 | 9674493 | C | T | 97.20% | 0.00% | C -> T | NA |
LOC_Os09g15840.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 92.645; most accessible tissue: Minghui63 panicle, score: 95.645 |
| vg0909674497 (J) | chr09 | 9674497 | C | T | 99.60% | 0.00% | C -> T | NA |
LOC_Os09g15840.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 92.598; most accessible tissue: Minghui63 panicle, score: 95.645 |
| vg0909674534 (J) | chr09 | 9674534 | G | C | 97.20% | 0.00% | G -> C | NA |
LOC_Os09g15840.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 92.383; most accessible tissue: Minghui63 panicle, score: 95.408 |
| vg0909674543 (J) | chr09 | 9674543 | G | A | 99.00% | 0.00% | G -> A | NA |
LOC_Os09g15840.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 92.173; most accessible tissue: Zhenshan97 flower, score: 95.157 |
| vg0909674546 (J) | chr09 | 9674546 | G | C | 76.20% | 0.02% | G -> C | NA |
LOC_Os09g15840.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g15840.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 92.119; most accessible tissue: Minghui63 panicle, score: 95.151 |
| vg0909674549 (J) | chr09 | 9674549 | G | C | 76.20% | 0.02% | G -> C | NA |
LOC_Os09g15840.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g15840.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 91.728; most accessible tissue: Zhenshan97 flower, score: 94.897 |
| vg0909674556 (J) | chr09 | 9674556 | C | T | 73.30% | 0.02% | C -> T | NA |
LOC_Os09g15840.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g15840.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 91.630; most accessible tissue: Zhenshan97 flower, score: 94.739 |
| vg0909674558 (J) | chr09 | 9674558 | GTT | G | 97.20% | 0.00% | GTT -> G | NA |
LOC_Os09g15840.1 Alt: G/frameshift_variant(CooVar)
The average chromatin accessibility score: 91.576; most accessible tissue: Zhenshan97 root, score: 94.742 |
| vg0909674561 (J) | chr09 | 9674561 | G | GCT | 97.20% | 0.00% | G -> GCT | NA |
The average chromatin accessibility score: 91.611; most accessible tissue: Zhenshan97 root, score: 94.742
|
| vg0909674570 (J) | chr09 | 9674570 | G | A | 97.20% | 0.00% | G -> A | NA |
LOC_Os09g15840.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 91.504; most accessible tissue: Zhenshan97 root, score: 94.742 |
| vg0909674579 (J) | chr09 | 9674579 | G | A | 97.20% | 0.00% | G -> A | NA |
LOC_Os09g15840.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 90.739; most accessible tissue: Zhenshan97 root, score: 94.723 |
| vg0909674593 (J) | chr09 | 9674593 | C | T | 97.20% | 0.00% | C -> T | NA |
LOC_Os09g15840.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 90.508; most accessible tissue: Zhenshan97 root, score: 94.723 |
| vg0909674609 (J) | chr09 | 9674609 | G | T | 75.00% | 21.43% | G -> T | NA |
LOC_Os09g15840.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g15840.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 89.899; most accessible tissue: Zhenshan97 root, score: 94.469 |
| vg0909674617 (J) | chr09 | 9674617 | T | TG | 74.80% | 24.95% | T -> TG | NA |
LOC_Os09g15840.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g15840.1 Alt: TG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 89.782; most accessible tissue: Zhenshan97 root, score: 94.364 |
| vg0909674623 (J) | chr09 | 9674623 | A | C | 74.70% | 24.88% | A -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g15840.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 89.202; most accessible tissue: Zhenshan97 root, score: 94.343 |
| vg0909674624 (J) | chr09 | 9674624 | A | G | 74.70% | 24.88% | A -> G | NA |
LOC_Os09g15840.1 Alt: G| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os09g15840.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 89.202; most accessible tissue: Zhenshan97 root, score: 94.343 |
| vg0909674636 (J) | chr09 | 9674636 | G | GCTAGGA GC | 73.10% | 23.74% | G -> GCTAGGAGC | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g15840.1 Alt: GCTAGGAGC| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 89.214; most accessible tissue: Zhenshan97 root, score: 94.343 |
| vg0909674648 (J) | chr09 | 9674648 | C | T | 72.90% | 24.33% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g15840.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 89.071; most accessible tissue: Zhenshan97 root, score: 94.490 |
| vg0909674668 (J) | chr09 | 9674668 | A | T | 73.10% | 23.89% | A -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g15840.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 88.373; most accessible tissue: Zhenshan97 root, score: 94.321 |