26 variations found. Os08g0101100/LOC_Os08g01100 (HMG1%2F2; putative; expressed), ranging from 71,342 bp to 72,715 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os08g01100 | HMG1/2, putative, expressed; RAP ID: Os08g0101100; MSU ID: LOC_Os08g01100 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0800071587 (J) | chr08 | 71587 | TAGA | T | 84.40% | 0.00% | TAGA -> T | NA |
LOC_Os08g01100.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g01090.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g01090.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0800071653 (J) | chr08 | 71653 | G | A | 96.80% | 0.00% | G -> A | NA |
LOC_Os08g01100.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g01090.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g01090.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0800071670 (J) | chr08 | 71670 | AAG | A | 94.50% | 0.00% | AAG -> A | NA |
LOC_Os08g01100.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g01090.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g01090.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0800071743 (J) | chr08 | 71743 | TTCC | T | 65.80% | 0.00% | T -> TTCC | NA |
LOC_Os08g01100.1 Alt: TTCC| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0800071768 (J) | chr08 | 71768 | T | C | 99.70% | 0.00% | T -> C | NA |
LOC_Os08g01100.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os08g01090.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os08g01090.2 Alt: C| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0800071799 (J) | chr08 | 71799 | A | G | 62.20% | 0.00% | G -> A |
mr1746 (All); LR P-value: 1.08E-13;
mr1746 (Jap_All); LR P-value: 2.49E-10; mr1769 (Jap_All); LR P-value: 6.69E-13; mr1790 (All); LR P-value: 1.05E-09; mr1805 (Jap_All); LR P-value: 1.42E-06; mr1019_2 (Jap_All); LR P-value: 1.55E-09; mr1039_2 (Jap_All); LR P-value: 6.10E-06; mr1401_2 (All); LR P-value: 1.75E-21; mr1401_2 (Jap_All); LR P-value: 2.72E-07; mr1558_2 (Jap_All); LR P-value: 3.67E-06; mr1632_2 (Jap_All); LR P-value: 2.37E-07; mr1676_2 (Jap_All); LR P-value: 6.12E-08; mr1746_2 (All); LR P-value: 1.22E-19; mr1746_2 (Jap_All); LR P-value: 1.35E-09; mr1885_2 (All); LR P-value: 2.21E-07; mr1924_2 (All); LR P-value: 2.00E-21 |
LOC_Os08g01100.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0800071830 (J) | chr08 | 71830 | A | G | 89.10% | 0.00% | A -> G |
LOC_Os08g01100.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
|
| vg0800071909 (J) | chr08 | 71909 | CA | C | 96.10% | 0.00% | CA -> C | NA |
LOC_Os08g01090.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g01090.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g01100.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0800071915 (J) | chr08 | 71915 | GAA | G | 99.70% | 0.00% | GAA -> G | NA |
LOC_Os08g01090.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os08g01090.2 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os08g01100.1 Alt: G| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0800072058 (J) | chr08 | 72058 | G | A | 61.70% | 0.28% | G -> A |
mr1057 (All); LR P-value: 5.19E-06;
mr1277 (All); LMM P-value: 8.87E-11; LR P-value: 6.62E-16; mr1277 (Ind_All); LMM P-value: 7.88E-10; LR P-value: 1.56E-08; mr1746 (All); LMM P-value: 3.17E-20; LR P-value: 1.67E-35; mr1746 (Ind_All); LMM P-value: 3.54E-15; LR P-value: 1.60E-20; mr1746 (Jap_All); LR P-value: 1.85E-11; mr1769 (Jap_All); LR P-value: 4.55E-13; mr1805 (Jap_All); LR P-value: 1.63E-06; mr1055_2 (Jap_All); LR P-value: 7.48E-13; mr1277_2 (All); LMM P-value: 5.64E-08; mr1277_2 (Ind_All); LMM P-value: 1.44E-06; mr1632_2 (Jap_All); LR P-value: 2.79E-07; mr1676_2 (Jap_All); LR P-value: 2.32E-08; mr1746_2 (All); LMM P-value: 5.48E-23; LR P-value: 1.49E-43; mr1746_2 (Ind_All); LMM P-value: 8.13E-19; LR P-value: 2.72E-27; mr1746_2 (Jap_All); LR P-value: 1.16E-09; mr1769_2 (Jap_All); LR P-value: 1.67E-13 |
LOC_Os08g01100.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g01100.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0800072129 (J) | chr08 | 72129 | ATCTTCT | A | 56.20% | 0.32% | ATCTTCT -> A,GTCTTCT, ATCT,ATCTT CTTCT | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os08g01090.1 Alt: ATCTTCTTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g01090.2 Alt: ATCTTCTTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g01100.1 Alt: ATCTTCTTCT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g01090.1 Alt: GTCTTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g01090.2 Alt: GTCTTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g01100.1 Alt: GTCTTCT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g01090.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g01090.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g01100.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g01090.1 Alt: ATCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g01090.2 Alt: ATCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g01100.1 Alt: ATCT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0800072138 (J) | chr08 | 72138 | T | TTCG | 61.70% | 0.28% | T -> TTCG | NA |
LOC_Os08g01090.1 Alt: TTCG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g01090.2 Alt: TTCG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g01100.1 Alt: TTCG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0800072179 (J) | chr08 | 72179 | T | C | 99.20% | 0.00% | T -> C | NA |
LOC_Os08g01090.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g01090.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g01100.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0800072210 (J) | chr08 | 72210 | G | A | 65.80% | 0.00% | A -> G |
mr1746 (Jap_All); LR P-value: 2.49E-10;
mr1769 (Jap_All); LR P-value: 6.69E-13; mr1805 (Jap_All); LR P-value: 1.42E-06; mr1019_2 (Jap_All); LR P-value: 1.55E-09; mr1039_2 (Jap_All); LR P-value: 6.10E-06; mr1401_2 (Jap_All); LR P-value: 2.72E-07; mr1558_2 (Jap_All); LR P-value: 3.67E-06; mr1632_2 (Jap_All); LR P-value: 2.37E-07; mr1676_2 (Jap_All); LR P-value: 6.12E-08; mr1746_2 (Jap_All); LR P-value: 1.35E-09 |
LOC_Os08g01100.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0800072259 (J) | chr08 | 72259 | T | C | 95.20% | 0.00% | T -> C | NA |
LOC_Os08g01100.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0800072268 (J) | chr08 | 72268 | CTCT | C | 95.30% | 0.00% | CTCT -> C | NA |
LOC_Os08g01100.1 Alt: C| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0800072285 (J) | chr08 | 72285 | C | T | 70.80% | 0.00% | T -> C |
mr1018 (All); LR P-value: 9.63E-74;
mr1228 (All); LR P-value: 4.71E-15; mr1235 (All); LR P-value: 8.39E-39; mr1243 (All); LR P-value: 1.30E-33; mr1277 (All); LR P-value: 1.03E-10; mr1423 (All); LR P-value: 6.70E-28; mr1533 (All); LR P-value: 2.89E-39; mr1653 (All); LR P-value: 1.19E-13; mr1746 (All); LR P-value: 3.63E-13; mr1746 (Jap_All); LR P-value: 4.27E-10; mr1778 (All); LR P-value: 1.40E-73; mr1784 (All); LR P-value: 7.26E-36; mr1805 (Jap_All); LR P-value: 5.05E-07; mr1980 (All); LR P-value: 1.18E-34; mr1019_2 (All); LR P-value: 1.92E-77; mr1217_2 (All); LR P-value: 4.98E-13; mr1232_2 (All); LR P-value: 3.06E-09; mr1261_2 (All); LR P-value: 6.51E-54; mr1277_2 (All); LR P-value: 3.37E-16; mr1298_2 (All); LR P-value: 2.84E-21; mr1308_2 (All); LR P-value: 3.70E-22; mr1489_2 (All); LR P-value: 9.31E-76; mr1510_2 (Jap_All); LR P-value: 3.06E-06; mr1529_2 (All); LR P-value: 1.23E-14; mr1533_2 (All); LR P-value: 8.00E-41; mr1575_2 (All); LR P-value: 9.19E-14; mr1632_2 (Jap_All); LR P-value: 3.14E-07; mr1653_2 (All); LR P-value: 9.17E-26; mr1659_2 (All); LR P-value: 6.87E-08; mr1676_2 (Jap_All); LR P-value: 1.06E-07; mr1682_2 (All); LR P-value: 5.39E-18; mr1730_2 (All); LR P-value: 4.23E-17; mr1731_2 (All); LR P-value: 1.45E-20; mr1746_2 (All); LR P-value: 4.44E-22; mr1746_2 (Jap_All); LR P-value: 2.01E-11; mr1778_2 (All); LR P-value: 1.29E-77; mr1805_2 (All); LR P-value: 3.66E-40; mr1866_2 (All); LR P-value: 4.74E-17; mr1986_2 (All); LR P-value: 8.76E-11 |
LOC_Os08g01100.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0800072288 (J) | chr08 | 72288 | C | A | 99.90% | 0.00% | C -> A | NA |
LOC_Os08g01100.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0800072331 (J) | chr08 | 72331 | G | C | 96.80% | 0.00% | G -> C | NA |
LOC_Os08g01090.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g01090.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g01100.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0800072380 (J) | chr08 | 72380 | AAG | A | 56.40% | 5.18% | AAG -> A,AAGAG,AA GAGAG | NA |
LOC_Os08g01090.1 Alt: AAGAGAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g01090.2 Alt: AAGAGAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g01100.1 Alt: AAGAGAG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g01090.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g01090.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g01100.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g01090.1 Alt: AAGAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g01090.2 Alt: AAGAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g01100.1 Alt: AAGAG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0800072385 (J) | chr08 | 72385 | A | AGG | 61.50% | 0.28% | A -> AGG | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os08g01090.1 Alt: AGG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g01090.2 Alt: AGG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g01100.1 Alt: AGG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0800072552 (J) | chr08 | 72552 | A | G | 76.20% | 0.19% | A -> G |
mr1277 (All); LMM P-value: 2.88E-08;
mr1277 (Ind_All); LMM P-value: 9.08E-09; LR P-value: 8.10E-08; mr1746 (All); LMM P-value: 1.34E-12; mr1746 (Ind_All); LMM P-value: 1.06E-13; LR P-value: 1.25E-17; mr1277_2 (All); LMM P-value: 1.56E-06; mr1277_2 (Ind_All); LMM P-value: 7.65E-07; mr1746_2 (All); LMM P-value: 8.47E-17; mr1746_2 (Ind_All); LMM P-value: 5.64E-19; LR P-value: 5.35E-25 |
LOC_Os08g01090.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g01090.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g01100.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0800072679 (J) | chr08 | 72679 | CAGAGGA GATG | C | 53.30% | 0.00% | C -> CAGAGGAGAT G,CCGAGGAG ATG | NA |
LOC_Os08g01100.1 Alt: CCGAGGAGATG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g01090.2 Alt: CCGAGGAGATG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g01100.1 Alt: CAGAGGAGATG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g01090.2 Alt: CAGAGGAGATG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0800072687 (J) | chr08 | 72687 | A | AT | 93.10% | 0.00% | A -> AT | NA |
LOC_Os08g01100.1 Alt: AT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g01090.2 Alt: AT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0800072688 (J) | chr08 | 72688 | G | GAGAGGA | 93.10% | 0.00% | G -> GAGAGGA,GA AAGGA | NA |
LOC_Os08g01100.1 Alt: GAAAGGA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g01090.2 Alt: GAAAGGA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g01100.1 Alt: GAGAGGA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g01090.2 Alt: GAGAGGA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| STR0800072269 (J) | chr08 | 72269 | TCTTCTT CTT | TCTTCTT | 94.80% | 0.00% | TCTTCTTCTT -> TCTTCTT | NA |
|