363 variations found. Os12g0552300/LOC_Os12g36620 (pentatricopeptide; putative; expressed), ranging from 22,419,757 bp to 22,427,185 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os12g36620 | pentatricopeptide, putative, expressed; RAP ID: Os12g0552300; MSU ID: LOC_Os12g36620 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| STR1222422571 (J) | chr12 | 22422571 | AATAAAT G | AATAAAT A | 53.60% | 0.00% | AATAAATA -> AATAAATG | NA |
|
| STR1222422913 (J) | chr12 | 22422913 | T | TT | 55.30% | 0.00% | TT -> T | NA |
|
| STR1222423567 (J) | chr12 | 22423567 | TCTCAAT CTGTCTG | TTTCAAT CTATCTG C | 72.10% | 0.00% | TCTCAATCTG TCTG -> TTTCAATCTA TCTGC | NA |
|
| STR1222424949 (J) | chr12 | 22424949 | TCCAATT CCAAT | TCTAATT CCAGT | 73.30% | 0.00% | TCCAATTCCA AT -> TCTAATTCCA GT,TCCAATT CCAGT | NA |
|
| STR1222425800 (J) | chr12 | 22425800 | CATTGCT | CATTGCA | 59.00% | 0.00% | CATTGCA -> CATTGCT | NA |
|
| STR1222426110 (J) | chr12 | 22426110 | CTAGTGC AAGTGCA AG | CCGGTGT AAGTGCA AG | 89.10% | 0.00% | CTAGTGCAAG TGCAAG -> CCGGTGTAAG TGCAAG,CCA GTGCAAGTGC AAG | NA |
|
| vg1222419776 (J) | chr12 | 22419776 | C | T | 52.00% | 42.87% | C -> T |
LOC_Os12g36620.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g36620.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 9.750; most accessible tissue: Callus, score: 56.791 |
|
| vg1222419795 (J) | chr12 | 22419795 | TAC | T | 43.00% | 42.34% | TAC -> T | NA |
LOC_Os12g36620.1 Alt: DEL/splice_acceptor_variant(CooVar)
LOC_Os12g36620.1 Alt: T| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os12g36600.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36610.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 9.666; most accessible tissue: Callus, score: 56.791 |
| vg1222419797 (J) | chr12 | 22419797 | C | T | 52.00% | 42.93% | C -> T |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g36620.1 Alt: T| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os12g36600.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36610.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 9.666; most accessible tissue: Callus, score: 56.791 |
|
| vg1222419829 (J) | chr12 | 22419829 | G | A | 31.20% | 43.93% | A -> G |
mr1180 (Jap_All); LR P-value: 5.60E-06;
mr1183 (Jap_All); LR P-value: 2.33E-06; mr1503 (Jap_All); LR P-value: 4.43E-06; mr1227_2 (All); LR P-value: 1.77E-06; mr1399_2 (All); LR P-value: 1.49E-07; mr1698_2 (All); LR P-value: 4.46E-22; mr1909_2 (All); LR P-value: 5.46E-08; mr1921_2 (All); LR P-value: 1.28E-07 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g36600.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36610.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36620.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 6.272; most accessible tissue: Callus, score: 19.452 |
| vg1222419871 (J) | chr12 | 22419871 | C | T | 31.30% | 43.91% | T -> C |
LOC_Os12g36600.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g36610.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36620.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 6.272; most accessible tissue: Callus, score: 19.452 |
|
| vg1222419888 (J) | chr12 | 22419888 | G | A | 31.40% | 43.42% | A -> G |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g36600.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36610.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36620.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 6.436; most accessible tissue: Callus, score: 19.452 |
|
| vg1222419894 (J) | chr12 | 22419894 | C | T | 56.10% | 42.55% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g36600.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36610.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36620.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 6.436; most accessible tissue: Callus, score: 19.452 |
| vg1222419915 (J) | chr12 | 22419915 | G | A | 31.40% | 42.89% | A -> G |
mr1013 (Ind_All); LR P-value: 2.29E-06;
mr1015 (Ind_All); LR P-value: 7.60E-07; mr1020 (Ind_All); LR P-value: 1.34E-06; mr1021 (All); LMM P-value: 4.29E-06; mr1021 (Ind_All); LR P-value: 4.09E-07; mr1031 (Ind_All); LR P-value: 4.60E-07; mr1032 (Ind_All); LR P-value: 1.42E-08; mr1050 (Ind_All); LR P-value: 3.57E-06; mr1056 (Ind_All); LR P-value: 2.92E-06; mr1066 (All); LR P-value: 1.14E-06; mr1126 (All); LR P-value: 3.60E-06; mr1140 (Jap_All); LR P-value: 4.43E-06; mr1165 (Ind_All); LR P-value: 2.89E-07; mr1291 (Ind_All); LR P-value: 2.16E-06; mr1477 (All); LMM P-value: 4.74E-06; mr1477 (Ind_All); LR P-value: 3.15E-08; mr1478 (Ind_All); LR P-value: 4.53E-08; mr1532 (All); LR P-value: 1.21E-06; mr1590 (Ind_All); LR P-value: 8.54E-06; mr1613 (Jap_All); LR P-value: 2.69E-06; mr1660 (Ind_All); LR P-value: 2.49E-06; mr1690 (All); LR P-value: 7.60E-07; mr1738 (All); LMM P-value: 7.44E-06; LR P-value: 1.00E-06; mr1755 (All); LMM P-value: 1.52E-06; LR P-value: 6.17E-07; mr1962 (Jap_All); LR P-value: 3.73E-06; mr1965 (Ind_All); LR P-value: 6.02E-06; mr1971 (Ind_All); LR P-value: 9.26E-06; mr1071_2 (Jap_All); LR P-value: 1.06E-06; mr1080_2 (Jap_All); LR P-value: 1.83E-06; mr1100_2 (Jap_All); LR P-value: 4.55E-07; mr1152_2 (Ind_All); LR P-value: 6.76E-06; mr1203_2 (Jap_All); LR P-value: 7.88E-08; mr1220_2 (Ind_All); LR P-value: 9.35E-06; mr1293_2 (All); LR P-value: 7.40E-06; mr1352_2 (Ind_All); LR P-value: 1.64E-09; mr1494_2 (All); LR P-value: 7.15E-06; mr1497_2 (All); LR P-value: 1.57E-06; mr1528_2 (All); LR P-value: 5.26E-06; mr1613_2 (Jap_All); LR P-value: 1.97E-07; mr1814_2 (All); LR P-value: 3.97E-06; mr1894_2 (All); LR P-value: 6.10E-06 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g36600.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36610.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36620.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 6.436; most accessible tissue: Callus, score: 19.452 |
| vg1222419954 (J) | chr12 | 22419954 | G | T | 31.40% | 42.89% | T -> G |
mr1013 (Ind_All); LR P-value: 4.80E-06;
mr1015 (Ind_All); LR P-value: 1.51E-06; mr1020 (All); LMM P-value: 9.26E-06; mr1020 (Ind_All); LR P-value: 1.14E-06; mr1021 (All); LMM P-value: 1.63E-06; mr1021 (Ind_All); LR P-value: 6.20E-07; mr1031 (Ind_All); LR P-value: 6.78E-07; mr1032 (Ind_All); LR P-value: 1.21E-08; mr1050 (Ind_All); LR P-value: 5.18E-06; mr1056 (Ind_All); LR P-value: 3.67E-06; mr1066 (All); LR P-value: 4.09E-06; mr1127 (All); LR P-value: 8.95E-06; mr1140 (Jap_All); LR P-value: 4.43E-06; mr1165 (Ind_All); LR P-value: 2.35E-07; mr1291 (Ind_All); LR P-value: 3.98E-06; mr1477 (All); LMM P-value: 1.77E-06; mr1477 (Ind_All); LR P-value: 6.57E-08; mr1478 (Ind_All); LR P-value: 6.36E-08; mr1532 (All); LR P-value: 2.72E-06; mr1590 (Ind_All); LR P-value: 5.30E-06; mr1613 (Jap_All); LR P-value: 2.69E-06; mr1660 (Ind_All); LR P-value: 1.24E-06; mr1690 (All); LR P-value: 6.34E-07; mr1738 (All); LR P-value: 1.08E-06; mr1755 (All); LMM P-value: 7.37E-07; LR P-value: 2.94E-07; mr1962 (Jap_All); LR P-value: 3.73E-06; mr1965 (Ind_All); LR P-value: 7.28E-06; mr1071_2 (Jap_All); LR P-value: 1.06E-06; mr1080_2 (Jap_All); LR P-value: 1.83E-06; mr1100_2 (Jap_All); LR P-value: 4.55E-07; mr1203_2 (Jap_All); LR P-value: 7.88E-08; mr1220_2 (Ind_All); LR P-value: 4.49E-06; mr1293_2 (All); LR P-value: 3.19E-06; mr1494_2 (All); LR P-value: 5.72E-06; mr1497_2 (All); LR P-value: 1.66E-06; mr1528_2 (All); LR P-value: 1.12E-06; mr1613_2 (Jap_All); LR P-value: 1.97E-07; mr1814_2 (All); LR P-value: 5.64E-06; mr1894_2 (All); LR P-value: 5.70E-06; mr1983_2 (All); LMM P-value: 4.34E-06; LR P-value: 4.35E-06 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g36600.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36610.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36620.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 10.616; most accessible tissue: Callus, score: 63.722 |
| vg1222419971 (J) | chr12 | 22419971 | G | A | 43.20% | 42.42% | G -> A,GT |
mr1057 (All); LR P-value: 9.34E-07;
mr1140 (Jap_All); LR P-value: 3.60E-06; mr1613 (Jap_All); LR P-value: 8.74E-07; mr1962 (Jap_All); LR P-value: 2.09E-06; mr1057_2 (All); LR P-value: 1.17E-07; mr1071_2 (Jap_All); LR P-value: 7.63E-07; mr1080_2 (Jap_All); LR P-value: 3.30E-06; mr1100_2 (Jap_All); LR P-value: 1.65E-07; mr1126_2 (All); LR P-value: 2.18E-09; mr1203_2 (Jap_All); LR P-value: 6.34E-08; mr1613_2 (Jap_All); LR P-value: 7.69E-08; mr1691_2 (Jap_All); LR P-value: 4.51E-06 |
LOC_Os12g36600.1 Alt: GT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g36610.1 Alt: GT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36620.1 Alt: GT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36600.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36610.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36620.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 10.616; most accessible tissue: Callus, score: 63.722 |
| vg1222419976 (J) | chr12 | 22419976 | G | A | 57.10% | 41.96% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g36600.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36610.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36620.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 10.692; most accessible tissue: Callus, score: 63.722 |
| vg1222420003 (J) | chr12 | 22420003 | A | ATG | 43.90% | 43.27% | A -> ATG | NA |
LOC_Os12g36600.1 Alt: ATG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g36610.1 Alt: ATG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36620.1 Alt: ATG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 11.110; most accessible tissue: Callus, score: 63.722 |
| vg1222420005 (J) | chr12 | 22420005 | A | G | 23.20% | 55.71% | A -> G |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g36600.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36610.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36620.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 11.110; most accessible tissue: Callus, score: 63.722 |
|
| vg1222420007 (J) | chr12 | 22420007 | GTT | G | 42.90% | 43.53% | GTT -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g36600.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36610.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36620.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 11.110; most accessible tissue: Callus, score: 63.722 |
| vg1222420009 (J) | chr12 | 22420009 | T | G | 24.50% | 55.54% | T -> G |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g36600.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36610.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36620.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 11.110; most accessible tissue: Callus, score: 63.722 |
|
| vg1222420013 (J) | chr12 | 22420013 | G | A | 38.20% | 43.59% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g36600.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36610.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36620.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 11.110; most accessible tissue: Callus, score: 63.722 |
| vg1222420039 (J) | chr12 | 22420039 | GA | G | 42.30% | 42.07% | GA -> G,AA | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g36600.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36610.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36620.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36600.1 Alt: AA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36610.1 Alt: AA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36620.1 Alt: AA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 11.240; most accessible tissue: Callus, score: 63.722 |
| vg1222420133 (J) | chr12 | 22420133 | A | G | 50.90% | 43.72% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g36620.1 Alt: A| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os12g36600.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36610.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 10.856; most accessible tissue: Callus, score: 57.458 |
| vg1222420538 (J) | chr12 | 22420538 | C | T | 38.80% | 43.31% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g36600.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36610.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g36620.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 13.735; most accessible tissue: Callus, score: 90.472 |
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