29 variations found. Os12g0571100/LOC_Os12g38300 (metallothionein; putative; expressed), ranging from 23,515,146 bp to 23,515,798 bp (including 0 kb upstream and 0 kb downstream of the gene).
| MSU ID | RAP ID | Symbol | Name | Explanation | Recommended Gene Symbol | Recommended Gene Name |
|---|---|---|---|---|---|---|
| LOC_Os12g38300 | Os12g0571100 | MT-1-4b, OsMT1d, OsMT-I-4c | metallochionein 1-4b, Metallothionein 1d, type 1 metallothionein d | type 1 small Cys-rich and metal binding protein, metallochionein. Q2QNC3. | MTI4C | METALLOTHIONEIN I-4C |
| 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1223515155 (J) | chr12 | 23515155 | C | T | 98.80% | 0.00% | C -> T | NA |
LOC_Os12g38300.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 57.760; most accessible tissue: Minghui63 root, score: 94.243 |
| vg1223515211 (J) | chr12 | 23515211 | G | A | 98.70% | 0.00% | G -> A | NA |
LOC_Os12g38310.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g38280.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38290.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38320.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38300.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 58.535; most accessible tissue: Minghui63 root, score: 92.361 |
| vg1223515223 (J) | chr12 | 23515223 | T | C | 98.70% | 0.00% | T -> C | NA |
LOC_Os12g38310.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g38280.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38290.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38320.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38300.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 58.523; most accessible tissue: Minghui63 root, score: 91.928 |
| vg1223515273 (J) | chr12 | 23515273 | C | G | 98.70% | 0.00% | C -> G | NA |
LOC_Os12g38310.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g38280.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38290.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38320.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38300.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 57.856; most accessible tissue: Minghui63 root, score: 88.642 |
| vg1223515277 (J) | chr12 | 23515277 | G | T | 95.60% | 0.00% | G -> T |
LOC_Os12g38310.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g38280.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38290.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38320.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38300.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 59.172; most accessible tissue: Minghui63 root, score: 88.829 |
|
| vg1223515300 (J) | chr12 | 23515300 | C | G | 98.70% | 0.00% | C -> G | NA |
LOC_Os12g38310.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g38280.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38290.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38320.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38300.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 61.732; most accessible tissue: Minghui63 root, score: 88.578 |
| vg1223515304 (J) | chr12 | 23515304 | G | T | 95.60% | 0.00% | G -> T | NA |
LOC_Os12g38310.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g38280.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38290.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38320.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38300.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 62.190; most accessible tissue: Minghui63 root, score: 88.578 |
| vg1223515363 (J) | chr12 | 23515363 | T | A | 98.70% | 0.00% | T -> A | NA |
LOC_Os12g38310.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g38280.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38290.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38320.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38300.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 63.719; most accessible tissue: Minghui63 root, score: 88.175 |
| vg1223515373 (J) | chr12 | 23515373 | CCATAAG ACAAAAA AAAAGTT GT | C | 99.00% | 0.00% | CCATAAGACA AAAAAAAAGT TGT -> C | NA |
LOC_Os12g38310.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
LOC_Os12g38280.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g38290.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g38320.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g38300.1 Alt: C| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 63.690; most accessible tissue: Minghui63 root, score: 88.106 |
| vg1223515381 (J) | chr12 | 23515381 | CA | CAA | 54.70% | 0.00% | CA -> CAA,CAAA,C | NA |
LOC_Os12g38310.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g38280.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38290.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38320.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38300.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38310.1 Alt: CAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38280.1 Alt: CAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38290.1 Alt: CAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38320.1 Alt: CAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38300.1 Alt: CAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38310.1 Alt: CAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38280.1 Alt: CAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38290.1 Alt: CAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38320.1 Alt: CAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38300.1 Alt: CAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 63.146; most accessible tissue: Minghui63 root, score: 87.745 |
| vg1223515392 (J) | chr12 | 23515392 | T | C | 96.80% | 0.00% | T -> C | NA |
LOC_Os12g38310.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g38280.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38290.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38320.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38300.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 62.345; most accessible tissue: Minghui63 root, score: 87.671 |
| vg1223515416 (J) | chr12 | 23515416 | T | C | 98.70% | 0.00% | T -> C | NA |
LOC_Os12g38310.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g38280.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38290.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38320.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38300.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 62.920; most accessible tissue: Minghui63 root, score: 87.745 |
| vg1223515418 (J) | chr12 | 23515418 | C | T | 98.70% | 0.00% | C -> T | NA |
LOC_Os12g38310.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g38280.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38290.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38320.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38300.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 62.676; most accessible tissue: Minghui63 root, score: 87.819 |
| vg1223515424 (J) | chr12 | 23515424 | GT | G | 98.70% | 0.00% | GT -> G | NA |
LOC_Os12g38310.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g38280.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38290.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38320.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38300.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 63.307; most accessible tissue: Minghui63 root, score: 87.892 |
| vg1223515431 (J) | chr12 | 23515431 | G | C | 98.70% | 0.00% | G -> C | NA |
LOC_Os12g38310.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g38280.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38290.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38320.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38300.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 66.456; most accessible tissue: Minghui63 root, score: 88.035 |
| vg1223515433 (J) | chr12 | 23515433 | T | C | 98.70% | 0.00% | T -> C | NA |
LOC_Os12g38310.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g38280.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38290.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38320.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38300.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 66.470; most accessible tissue: Minghui63 root, score: 88.035 |
| vg1223515442 (J) | chr12 | 23515442 | T | C | 95.60% | 0.00% | T -> C |
LOC_Os12g38300.1 Alt: C| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os12g38310.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38280.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38290.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38320.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 67.065; most accessible tissue: Minghui63 root, score: 88.313 |
|
| vg1223515451 (J) | chr12 | 23515451 | T | A | 97.70% | 0.00% | T -> A | NA |
LOC_Os12g38300.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 66.222; most accessible tissue: Minghui63 root, score: 87.964 |
| vg1223515462 (J) | chr12 | 23515462 | C | T | 97.70% | 0.00% | C -> T | NA |
LOC_Os12g38300.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 66.141; most accessible tissue: Minghui63 root, score: 87.819 |
| vg1223515537 (J) | chr12 | 23515537 | A | G | 99.40% | 0.00% | A -> G | NA |
LOC_Os12g38310.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os12g38280.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g38290.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g38320.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g38300.1 Alt: G| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 72.982; most accessible tissue: Minghui63 root, score: 89.417 |
| vg1223515567 (J) | chr12 | 23515567 | T | C | 99.80% | 0.00% | T -> C | NA |
LOC_Os12g38310.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
LOC_Os12g38280.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g38290.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g38320.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g38300.1 Alt: C| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 74.670; most accessible tissue: Minghui63 root, score: 89.793 |
| vg1223515576 (J) | chr12 | 23515576 | T | TA | 96.60% | 0.00% | T -> TA | NA |
LOC_Os12g38310.1 Alt: TA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g38280.1 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38290.1 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38320.1 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38300.1 Alt: TA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 74.477; most accessible tissue: Minghui63 root, score: 90.186 |
| vg1223515596 (J) | chr12 | 23515596 | A | T | 98.70% | 0.00% | A -> T | NA |
LOC_Os12g38310.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g38290.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38320.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38300.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.466; most accessible tissue: Minghui63 root, score: 90.642 |
| vg1223515664 (J) | chr12 | 23515664 | C | G | 98.80% | 0.00% | C -> G | NA |
LOC_Os12g38310.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g38290.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38320.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38300.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.681; most accessible tissue: Minghui63 root, score: 91.181 |
| vg1223515671 (J) | chr12 | 23515671 | G | T | 98.80% | 0.00% | G -> T | NA |
LOC_Os12g38310.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g38290.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38320.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38300.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.652; most accessible tissue: Minghui63 root, score: 91.220 |
| vg1223515672 (J) | chr12 | 23515672 | A | C | 98.80% | 0.00% | A -> C | NA |
LOC_Os12g38300.1 Alt: C| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os12g38310.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38290.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38320.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.773; most accessible tissue: Minghui63 root, score: 91.220 |
| vg1223515675 (J) | chr12 | 23515675 | T | G | 59.50% | 0.00% | T -> G | NA |
LOC_Os12g38300.1 Alt: G| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os12g38310.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38290.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g38320.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.672; most accessible tissue: Minghui63 root, score: 91.220 |
| vg1223515705 (J) | chr12 | 23515705 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os12g38300.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os12g38310.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g38290.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g38320.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 80.623; most accessible tissue: Minghui63 root, score: 91.517 |
| STR1223515577 (J) | chr12 | 23515577 | AAA | AAAA | 93.70% | 0.00% | AAA -> AAAA | NA |
|