mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 77,405 | G→T | 100% | noncoding (39/227 nt) Q6H (CAG→CAT) |
sgrS → sgrT → |
sRNA antisense regulator destabilzes ptsG mRNA, Hfq‑dependent; regulated by sgrR inhibitor of glucose uptake |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 378,398 | A→G | 7.3% | intergenic (‑30/+64) | frmB ← / ← frmA | S‑formylglutathione hydrolase/alcohol dehydrogenase class III; glutathione‑dependent formaldehyde dehydrogenase |
| RA | 378,400 | G→A | 7.2% | intergenic (‑32/+62) | frmB ← / ← frmA | S‑formylglutathione hydrolase/alcohol dehydrogenase class III; glutathione‑dependent formaldehyde dehydrogenase |
| RA | 378,403 | T→C | 7.2% | intergenic (‑35/+59) | frmB ← / ← frmA | S‑formylglutathione hydrolase/alcohol dehydrogenase class III; glutathione‑dependent formaldehyde dehydrogenase |
| RA | 378,405 | C→T | 7.1% | intergenic (‑37/+57) | frmB ← / ← frmA | S‑formylglutathione hydrolase/alcohol dehydrogenase class III; glutathione‑dependent formaldehyde dehydrogenase |
| RA | 393,625 | C→T | 5.1% | pseudogene (656/1449 nt) | yaiT → | pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein |
| RA | 545,104 | G→A | 5.5% | Y63Y (TAC→TAT) | allC ← | allantoate amidohydrolase |
| RA | 606,072 | T→C | 5.8% | H43R (CAT→CGT) | ybdJ ← | DUF1158 family putative inner membrane protein |
| RA | 760,151 | A→G | 19.1% | T482T (ACA→ACG) | sucA → | 2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding |
| RA | 760,166 | C→T | 18.2% | Y487Y (TAC→TAT) | sucA → | 2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding |
| RA | 760,313 | C→T | 10.4% | Y536Y (TAC→TAT) | sucA → | 2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding |
| RA | 772,500 | A→G | 6.5% | K348R (AAG→AGG) | cydA → | cytochrome d terminal oxidase, subunit I |
| RA | 806,105 | C→T | 5.3% | D393N (GAT→AAT) | ybhC ← | acyl‑CoA thioesterase, lipoprotein |
| RA | 1,012,756 | C→A | 6.4% | S252R (AGC→AGA) | pqiA → | paraquat‑inducible, SoxRS‑regulated inner membrane protein |
| RA | 1,147,986 | G→C | 6.9% | L122L (CTG→CTC) | plsX → | putative phosphate acyltransferase |
| RA | 1,147,987 | G→C | 6.9% | E123Q (GAG→CAG) | plsX → | putative phosphate acyltransferase |
| RA | 1,147,993 | A→C | 6.8% | I125L (ATT→CTT) | plsX → | putative phosphate acyltransferase |
| RA | 1,476,874 | C→T | 5.0% | H577H (CAC→CAT) | ydbD → | PF10971 family putative periplasmic methylglyoxal resistance protein |
| RA | 1,529,175 | T→C | 100% | pseudogene (1274/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,180 | T→C | 100% | pseudogene (1279/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,185 | C→T | 100% | pseudogene (1284/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,203 | C→A | 100% | pseudogene (1302/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,218 | C→T | 100% | pseudogene (1317/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,622,833 | A→T | 5.7% | noncoding (82/98 nt) | mgrR ← | sRNA antisense regulator down regulates YgdQ and EptB, PhoPQ‑regulated, Hfq‑dependent; affects sensitivity to antimicrobial peptides |
| RA | 1,622,834 | A→T | 5.7% | noncoding (81/98 nt) | mgrR ← | sRNA antisense regulator down regulates YgdQ and EptB, PhoPQ‑regulated, Hfq‑dependent; affects sensitivity to antimicrobial peptides |
| RA | 1,622,837 | C→T | 5.7% | noncoding (78/98 nt) | mgrR ← | sRNA antisense regulator down regulates YgdQ and EptB, PhoPQ‑regulated, Hfq‑dependent; affects sensitivity to antimicrobial peptides |
| RA | 1,746,551 | A→T | 6.1% | noncoding (36/77 nt) | valW → | tRNA‑Val |
| RA | 1,792,465 | G→A | 5.2% | G89G (GGC→GGT) | nlpC ← | putative C40 clan peptidase lipoprotein |
| RA | 1,959,465 | G→T | 8.3% | R128S (CGT→AGT) | yecM ← | putative metal‑binding enzyme |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,684,404 | C→T | 10.5% | A368A (GCG→GCA) | glyA ← | serine hydroxymethyltransferase |
| JC JC | 2,760,805 | IS2 (+) +5 bp | 100% | coding (259‑263/627 nt) | yfjJ → | CP4‑57 prophage; uncharacterized protein |
| RA | 3,068,537 | G→A | 7.3% | A91V (GCA→GTA) | argO ← | arginine transporter |
| RA | 3,093,643 | A→T | 7.4% | L48F (TTA→TTT) | yqgF → | putative Holliday junction resolvase |
| RA | 3,156,591 | T→G | 6.0% | intergenic (+73/‑32) | yqhD → / → dkgA | aldehyde reductase, NADPH‑dependent/2,5‑diketo‑D‑gluconate reductase A |
| RA | 3,545,785 | A→T | 15.5% | T54T (ACA→ACT) | nfuA → | Fe/S biogenesis protein, putative scaffold/chaperone protein |
| RA | 3,545,860 | T→C | 24.3% | D79D (GAT→GAC) | nfuA → | Fe/S biogenesis protein, putative scaffold/chaperone protein |
| RA | 3,545,884 | C→T | 27.4% | S87S (TCC→TCT) | nfuA → | Fe/S biogenesis protein, putative scaffold/chaperone protein |
| RA | 3,545,902 | C→G | 27.2% | A93A (GCC→GCG) | nfuA → | Fe/S biogenesis protein, putative scaffold/chaperone protein |
| RA | 3,545,905 | G→T | 27.9% | P94P (CCG→CCT) | nfuA → | Fe/S biogenesis protein, putative scaffold/chaperone protein |
| RA | 3,546,088 | C→G | 31.0% | V155V (GTC→GTG) | nfuA → | Fe/S biogenesis protein, putative scaffold/chaperone protein |
| RA | 3,546,127 | G→A | 29.0% | L168L (CTG→CTA) | nfuA → | Fe/S biogenesis protein, putative scaffold/chaperone protein |
| RA | 3,560,455:1 | +G | 100% | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,828,165 | G→T | 6.4% | F167L (TTC→TTA) | gltS ← | glutamate transporter |
| RA | 3,941,891 | T→A | 8.0% | noncoding (84/1542 nt) | rrsC → | 16S ribosomal RNA of rrnC operon |
| RA | 3,941,892 | T→A | 8.0% | noncoding (85/1542 nt) | rrsC → | 16S ribosomal RNA of rrnC operon |
| RA | 3,980,643 | C→T | 6.6% | R230C (CGT→TGT) | wecG → | UDP‑N‑acetyl‑D‑mannosaminuronic acid transferase |
| RA | 4,070,814 | G→T | 100% | R315S (CGT→AGT) | yihS ← | sulphoquinovose isomerase |
| RA | 4,070,817 | C→A | 100% | V314L (GTA→TTA) | yihS ← | sulphoquinovose isomerase |
| RA | 4,075,154 | Δ2 bp | 100% | coding (486‑487/786 nt) | yihW → | putative transcriptional regulator for sulphoquinovose utilization |
| RA | 4,148,049 | C→G | 8.3% | G90A (GGC→GCC) | yijO ← | AraC family putative transcriptional activator |
| RA | 4,178,482 | G→A | 6.2% | Q12Q (CAG→CAA) | rplK → | 50S ribosomal subunit protein L11 |
| RA | 4,178,484 | T→C | 6.1% | V13A (GTT→GCT) | rplK → | 50S ribosomal subunit protein L11 |
| RA | 4,184,557 | T→C | 100% | S1105P (TCT→CCT) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,283,320:1 | +CA | 100% | coding (1583/1650 nt) | actP ← | acetate transporter |
| RA | 4,296,190 | A→G | 17.8% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 14.8% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 33.2% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 29.3% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,303 | A→G | 22.2% | intergenic (+509/+133) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,304 | A→C | 17.5% | intergenic (+510/+132) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,393,339 | A→T | 9.1% | I243I (ATT→ATA) | queG ← | epoxyqueuosine reductase, cobalamine‑stimulated; queosine biosynthesis |
| RA | 4,474,747 | C→T | 6.7% | intergenic (+30/‑115) | bdcR → / → tabA | transcriptional repressor for divergent bdcA/biofilm modulator regulated by toxins; DUF386 family protein, cupin superfamily protein |
| RA | 4,501,959 | C→T | 5.5% | intergenic (+370/+144) | yjgZ → / ← insG | uncharacterized protein/IS4 transposase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423828–3424234 | 3424433–3424238 | 5–606 | 20 [18] | [18] 19 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 41 (0.670) | 17 (0.300) | 17/530 | NT | 32.5% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 32 (0.560) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 42 (0.690) | 15 (0.260) | 15/530 | NT | 29.5% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 32 (0.560) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 110 (1.830) | 97/554 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 1562837 = | 47 (0.770) | 4 (0.070) | 3/546 | NT | 8.2% | coding (240/582 nt) | ddpX | D‑ala‑D‑ala dipeptidase, Zn‑dependent |
| ? | NC_000913 | 1562864 = | 44 (0.740) | coding (213/582 nt) | ddpX | D‑ala‑D‑ala dipeptidase, Zn‑dependent | |||||
| * | ? | NC_000913 | 3150551 = | NA (NA) | 3 (0.050) | 3/540 | NT | NA | intergenic (+5/+267) | yghA/exbD | putative oxidoreductase/membrane spanning protein in TonB‑ExbB‑ExbD complex |
| ? | NC_000913 | 3150580 = | NA (NA) | noncoding (27/255 nt) | RIP222 (repetitive extragenic palindromic) element; contains 5 REP sequences and 2 IHF sites | RIP222 (repetitive extragenic palindromic) element; contains 5 REP sequences and 2 IHF sites | |||||