103 variations found. LOC_Os02g34600 (CAMK_CAMK_like.13 - CAMK includes calcium%2Fcalmodulin depedent protein kinases; expressed), ranging from 20,746,261 bp to 20,751,379 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 |
|---|---|---|---|---|---|---|---|---|---|
| STR0220746779 (J) | chr02 | 20746779 | CCTCCTC CTC | CCTCCTC | 87.30% | 0.00% | CCTCCTCCTC -> CCTCCTC | NA |
|
| STR0220747801 (J) | chr02 | 20747801 | TT | TC | 50.00% | 0.00% | TT -> TC | NA |
|
| STR0220750054 (J) | chr02 | 20750054 | AAA | AAAA | 50.00% | 0.00% | AAA -> AAAA | NA |
|
| STR0220750438 (J) | chr02 | 20750438 | TT | TT | 97.80% | 0.00% | TT -> TTT | NA |
|
| vg0220746293 (J) | chr02 | 20746293 | A | G | 72.30% | 0.00% | G -> A |
Grain_weight (All); LR P-value: 2.65E-11;
mr1754 (All); LR P-value: 6.85E-19; mr1668_2 (All); LR P-value: 4.16E-07 |
LOC_Os02g34600.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g34600.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 57.282; most accessible tissue: Minghui63 young leaf, score: 92.723 |
| vg0220746402 (J) | chr02 | 20746402 | A | G | 63.00% | 0.00% | G -> A,T | NA |
LOC_Os02g34600.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g34600.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g34600.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g34600.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 60.481; most accessible tissue: Minghui63 young leaf, score: 93.167 |
| vg0220746434 (J) | chr02 | 20746434 | C | T | 72.40% | 0.00% | T -> C |
Grain_weight (All); LMM P-value: 4.85E-06; LR P-value: 1.24E-11;
mr1754 (All); LR P-value: 6.03E-19; mr1921 (All); LR P-value: 2.94E-10; mr1668_2 (All); LR P-value: 4.49E-07 |
LOC_Os02g34600.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g34600.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.548; most accessible tissue: Minghui63 young leaf, score: 93.647 |
| vg0220746518 (J) | chr02 | 20746518 | AAAAAGA ACAGGAT | A | 99.80% | 0.00% | AAAAAGAACA GGAT -> A | NA |
LOC_Os02g34600.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os02g34600.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff) The average chromatin accessibility score: 76.793; most accessible tissue: Minghui63 young leaf, score: 95.017 |
| vg0220746522 (J) | chr02 | 20746522 | AGAACAG GAT | AAACAGG AT | 96.40% | 0.00% | AGAACAGGAT -> AAACAGGAT, A | NA |
LOC_Os02g34600.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g34600.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g34600.1 Alt: AAACAGGAT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g34600.2 Alt: AAACAGGAT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 77.045; most accessible tissue: Minghui63 young leaf, score: 95.066 |
| vg0220746523 (J) | chr02 | 20746523 | GAACAGG ATA | AAACAGG ATA | 93.50% | 0.00% | GAACAGGATA -> AAACAGGATA ,G | NA |
LOC_Os02g34600.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g34600.2 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g34600.1 Alt: AAACAGGATA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g34600.2 Alt: AAACAGGATA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.717; most accessible tissue: Minghui63 young leaf, score: 95.017 |
| vg0220746524 (J) | chr02 | 20746524 | AACAGGA T | A | 99.20% | 0.00% | AACAGGAT -> A,AAGGAT | NA |
LOC_Os02g34600.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g34600.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g34600.1 Alt: AAGGAT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g34600.2 Alt: AAGGAT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.977; most accessible tissue: Minghui63 young leaf, score: 95.115 |
| vg0220746525 (J) | chr02 | 20746525 | ACAGGAT | A | 91.80% | 0.00% | ACAGGAT -> A,AAGGAT,A AT | NA |
LOC_Os02g34600.1 Alt: AAT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g34600.2 Alt: AAT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g34600.1 Alt: AAGGAT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g34600.2 Alt: AAGGAT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g34600.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g34600.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.699; most accessible tissue: Minghui63 young leaf, score: 95.066 |
| vg0220746528 (J) | chr02 | 20746528 | GGATA | G | 99.00% | 0.00% | GGATA -> G,AGATA | NA |
LOC_Os02g34600.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g34600.2 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g34600.1 Alt: AGATA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g34600.2 Alt: AGATA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 77.361; most accessible tissue: Minghui63 young leaf, score: 95.210 |
| vg0220746578 (J) | chr02 | 20746578 | A | G | 88.00% | 0.00% | A -> G | NA |
LOC_Os02g34600.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g34600.2 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 81.066; most accessible tissue: Minghui63 young leaf, score: 95.984 |
| vg0220746695 (J) | chr02 | 20746695 | C | G | 91.40% | 0.00% | C -> G |
LOC_Os02g34600.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g34600.2 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 84.718; most accessible tissue: Minghui63 young leaf, score: 95.967 |
|
| vg0220746778 (J) | chr02 | 20746778 | CCCT | C | 88.10% | 0.00% | CCCT -> C | NA |
LOC_Os02g34600.1 Alt: C| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 85.493; most accessible tissue: Minghui63 young leaf, score: 96.323 |
| vg0220746946 (J) | chr02 | 20746946 | G | C | 72.40% | 0.00% | C -> G |
Grain_weight (All); LMM P-value: 4.85E-06; LR P-value: 1.24E-11;
mr1754 (All); LR P-value: 6.03E-19; mr1921 (All); LR P-value: 2.94E-10; mr1668_2 (All); LR P-value: 4.49E-07 |
LOC_Os02g34600.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 82.337; most accessible tissue: Minghui63 young leaf, score: 95.539 |
| vg0220747087 (J) | chr02 | 20747087 | AAATGGA ACAT | A | 66.20% | 0.00% | AAATGGAACA T -> A | NA |
LOC_Os02g34600.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g34600.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 73.709; most accessible tissue: Minghui63 young leaf, score: 93.394 |
| vg0220747127 (J) | chr02 | 20747127 | TA | T | 72.40% | 0.00% | T -> TA | NA |
LOC_Os02g34600.1 Alt: TA| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os02g34600.2 Alt: TA| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 72.627; most accessible tissue: Minghui63 young leaf, score: 93.394 |
| vg0220747129 (J) | chr02 | 20747129 | CATCTTC AGTGGAT | C | 62.60% | 0.00% | C -> CATCTTCAGT GGAT | NA |
The average chromatin accessibility score: 72.643; most accessible tissue: Minghui63 young leaf, score: 93.394
|
| vg0220747131 (J) | chr02 | 20747131 | C | T | 49.80% | 41.85% | C -> T | NA |
LOC_Os02g34600.1 Alt: T| splice_donor_variant&intron_variant HIGH(snpEff)/splice_donor_variant(CooVar)
LOC_Os02g34600.1 Alt: DEL/splice_donor_variant(CooVar) The average chromatin accessibility score: 72.643; most accessible tissue: Minghui63 young leaf, score: 93.394 |
| vg0220747356 (J) | chr02 | 20747356 | G | T | 66.20% | 0.00% | T -> G,A | NA |
LOC_Os02g34600.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g34600.2 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os02g34600.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os02g34600.2 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 66.331; most accessible tissue: Minghui63 young leaf, score: 89.871 |
| vg0220747383 (J) | chr02 | 20747383 | G | A | 90.10% | 0.00% | G -> A |
LOC_Os02g34600.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g34600.2 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 65.839; most accessible tissue: Minghui63 young leaf, score: 90.072 |
|
| vg0220747452 (J) | chr02 | 20747452 | T | A | 88.20% | 0.00% | T -> A | NA |
LOC_Os02g34600.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g34600.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.405; most accessible tissue: Minghui63 young leaf, score: 90.541 |
| vg0220747486 (J) | chr02 | 20747486 | T | C | 72.40% | 0.00% | C -> T |
Grain_weight (All); LMM P-value: 4.85E-06; LR P-value: 1.24E-11;
mr1754 (All); LR P-value: 6.03E-19; mr1921 (All); LR P-value: 2.94E-10; mr1668_2 (All); LR P-value: 4.49E-07 |
LOC_Os02g34600.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g34600.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.924; most accessible tissue: Minghui63 young leaf, score: 90.072 |
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