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 | 30,243 | A→G | 5.9% | V583V (GTA→GTG) | carB → | carbamoyl‑phosphate synthase large subunit |
| RA | 30,250 | T→G | 6.0% | S586A (TCG→GCG) | carB → | carbamoyl‑phosphate synthase large subunit |
| RA | 30,273 | T→C | 6.5% | G593G (GGT→GGC) | carB → | carbamoyl‑phosphate synthase large subunit |
| RA | 138,668 | G→A | 7.0% | S500L (TCA→TTA) | htrE ← | predicted outer membrane usher protein |
| RA | 138,670 | G→T | 6.3% | Y499* (TAC→TAA) | htrE ← | predicted outer membrane usher protein |
| RA | 138,673 | A→C | 6.4% | N498K (AAT→AAG) ‡ | htrE ← | predicted outer membrane usher protein |
| RA | 138,675 | T→C | 6.0% | N498D (AAT→GAT) ‡ | htrE ← | predicted outer membrane usher protein |
| RA | 204,511 | C→T | 100% | intergenic (+111/‑73) | alaV → / → rrlH | tRNA‑Ala/23S ribosomal RNA |
| RA | 204,556 | A→G | 100% | intergenic (+156/‑28) | alaV → / → rrlH | tRNA‑Ala/23S ribosomal RNA |
| RA | 214,925 | A→C | 33.4% | D12A (GAT→GCT) | dnaQ → | DNA polymerase III epsilon subunit |
| RA | 214,931 | A→C | 33.5% | E14A (GAA→GCA) | dnaQ → | DNA polymerase III epsilon subunit |
| RA | 1,036,505 | G→A | 100% | A632A (GCG→GCA) | rsxC → | fused predicted 4Fe‑4S ferredoxin‑type protein |
| RA | 1,221,878 | A→G | 5.9% | Q151Q (CAA→CAG) | yebT → | conserved hypothetical protein |
| RA | 1,221,883 | A→T | 6.0% | K153I (AAA→ATA) | yebT → | conserved hypothetical protein |
| RA | 1,221,886 | A→T | 6.4% | Y154F (TAT→TTT) | yebT → | conserved hypothetical protein |
| RA | 1,221,891 | C→T | 6.1% | L156L (CTG→TTG) | yebT → | conserved hypothetical protein |
| RA | 1,318,494 | C→A | 8.1% | R29L (CGT→CTT) | cld ← | regulator of length of O‑antigen component of lipopolysaccharide chains |
| RA | 1,763,556 | T→C | 43.8% | noncoding (288/1542 nt) | rrsG ← | 16S ribosomal RNA |
| RA | 1,763,558 | G→C | 8.4% | noncoding (286/1542 nt) | rrsG ← | 16S ribosomal RNA |
| RA | 1,763,636 | A→G | 33.3% | noncoding (208/1542 nt) | rrsG ← | 16S ribosomal RNA |
| RA | 1,804,090 | G→A | 26.8% | G52G (GGG→GGA) | mprA → | DNA‑binding transcriptional regulator |
| RA | 1,826,740 | G→T | 7.6% | intergenic (‑417/‑18) | hydN ← / → mutS | formate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit/methyl‑directed mismatch repair protein |
| RA | 1,826,741 | G→A | 7.7% | intergenic (‑418/‑17) | hydN ← / → mutS | formate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit/methyl‑directed mismatch repair protein |
| RA | 1,849,373 | A→T | 5.5% | V166E (GTG→GAG) | ygcH ← | hypothetical protein |
| RA | 1,892,019:1 | +GC | 100% | intergenic (‑437/+54) | gudP ← / ← ygdL | predicted D‑glucarate transporter/conserved hypothetical protein |
| RA | 2,256,801 | T→C | 5.4% | K79K (AAA→AAG) | rpoC ← | RNA polymerase, beta prime subunit |
| RA | 2,256,819 | A→G | 7.6% | G73G (GGT→GGC) | rpoC ← | RNA polymerase, beta prime subunit |
| RA | 2,256,831 | C→T | 6.0% | E69E (GAG→GAA) | rpoC ← | RNA polymerase, beta prime subunit |
| RA | 2,256,859 | C→T | 5.8% | R60H (CGT→CAT) | rpoC ← | RNA polymerase, beta prime subunit |
| RA | 2,359,867 | G→A | 28.4% | noncoding (1228/2905 nt) | rrlA ← | 23S ribosomal RNA |
| RA | 2,359,876 | C→T | 32.2% | noncoding (1219/2905 nt) | rrlA ← | 23S ribosomal RNA |
| RA | 2,518,841 | A→T | 7.2% | T78T (ACT→ACA) | spoT ← | bifunctional (p)ppGpp synthetase II and guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
| RA | 2,518,856 | G→A | 7.2% | D73D (GAC→GAT) | spoT ← | bifunctional (p)ppGpp synthetase II and guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
| RA | 2,567,260 | T→C | 5.9% | intergenic (‑209/+21) | mtlD ← / ← mtlA | mannitol‑1‑phosphate dehydrogenase, NAD(P)‑binding/fused mannitol‑specific PTS enzyme IIABC components |
| RA | 2,567,261 | G→A | 5.9% | intergenic (‑210/+20) | mtlD ← / ← mtlA | mannitol‑1‑phosphate dehydrogenase, NAD(P)‑binding/fused mannitol‑specific PTS enzyme IIABC components |
| RA | 2,726,575 | A→G | 6.9% | L170L (TTG→CTG) | yheS ← | fused predicted transporter subunits and ATP‑binding components of ABC superfamily |
| RA | 2,726,579 | T→G | 6.5% | S168S (TCA→TCC) | yheS ← | fused predicted transporter subunits and ATP‑binding components of ABC superfamily |
| RA | 2,726,583 | C→G | 7.0% | R167P (CGT→CCT) | yheS ← | fused predicted transporter subunits and ATP‑binding components of ABC superfamily |
| RA | 2,726,588 | A→C | 7.5% | I165M (ATT→ATG) | yheS ← | fused predicted transporter subunits and ATP‑binding components of ABC superfamily |
| RA | 2,726,600 | G→C | 7.2% | A161A (GCC→GCG) | yheS ← | fused predicted transporter subunits and ATP‑binding components of ABC superfamily |
| RA | 2,726,603 | A→C | 7.7% | L160L (CTT→CTG) | yheS ← | fused predicted transporter subunits and ATP‑binding components of ABC superfamily |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | Exported | 251992 | 252057 | 66 | 21 [16] | [16] 18 | malZ | maltodextrin glucosidase |
| * | * | ÷ | Exported | 444383 | 444419 | 37 | 17 [15] | [16] 19 | kdpE | DNA‑binding response regulator in two‑component regulatory system with KdpD |
| * | * | ÷ | Exported | 865545 | 865591 | 47 | 17 [16] | [16] 20 | yciQ | predicted inner membrane protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | Exported | = 7063 | 59 (0.840) | 30 (0.460) +GATT |
9/92 | NT | 49.0% | coding (897/1431 nt) | yaaJ | predicted transporter |
| ? | Exported | = 1611756 | 9 (0.130) | coding (1397/1404 nt) | eutA | reactivating factor for ethanolamine ammonia lyase | |||||
| * | ? | Exported | 26935 = | 32 (0.450) | 3 (0.050) | 3/78 | NT | 7.4% | intergenic (+62/‑394) | dapB/carA | dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase |
| ? | Exported | 26998 = | 50 (0.910) | intergenic (+125/‑331) | dapB/carA | dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase | |||||
| * | ? | Exported | 95427 = | 92 (1.300) | 10 (0.160) | 3/90 | NT | 11.1% | coding (2409/2706 nt) | secA | preprotein translocase subunit, ATPase that targets protein precursors to the SecYE core translocon |
| ? | Exported | 95453 = | 77 (1.210) | coding (2435/2706 nt) | secA | preprotein translocase subunit, ATPase that targets protein precursors to the SecYE core translocon | |||||
| * | ? | Exported | 204058 = | NA (NA) | 4 (0.060) | 3/92 | NT | NA | noncoding (1463/1542 nt) | rrsH | 16S ribosomal RNA |
| ? | Exported | 204096 = | NA (NA) | noncoding (1501/1542 nt) | rrsH | 16S ribosomal RNA | |||||
| * | ? | Exported | = 204740 | NA (NA) | 14 (0.240) | 6/84 | NT | NA | noncoding (157/2904 nt) | rrlH | 23S ribosomal RNA |
| ? | Exported | = 204751 | NA (NA) | noncoding (168/2904 nt) | rrlH | 23S ribosomal RNA | |||||
| * | ? | Exported | = 205293 | NA (NA) | 6 (0.090) | 3/92 | NT | NA | noncoding (710/2904 nt) | rrlH | 23S ribosomal RNA |
| ? | Exported | = 205316 | NA (NA) | noncoding (733/2904 nt) | rrlH | 23S ribosomal RNA | |||||
| * | ? | Exported | 436259 = | 64 (0.910) | 24 (0.370) | 14/92 | NT | 30.2% | intergenic (‑156/‑29) | ybfF/seqA | conserved hypothetical protein/regulatory protein for replication initiation |
| ? | Exported | = 2706018 | 52 (0.800) | coding (836/837 nt) | dam | DNA adenine methylase | |||||
| * | ? | Exported | = 436833 | 94 (1.330) | 61 (0.860) | 30/100 | NT | 41.8% | coding (546/546 nt) | seqA | regulatory protein for replication initiation |
| ? | Exported | 1803907 = | 76 (1.080) | intergenic (+63/‑28) | ygaH/mprA | predicted inner membrane protein/DNA‑binding transcriptional regulator | |||||
| * | ? | Exported | = 689805 | 61 (0.860) | 5 (0.080) | 3/92 | NT | 7.9% | coding (968/1119 nt) | hyaA | hydrogenase 1, small subunit |
| ? | Exported | = 689836 | 60 (0.920) | coding (999/1119 nt) | hyaA | hydrogenase 1, small subunit | |||||
| * | ? | Exported | 825034 = | 64 (0.910) | 5 (0.080) | 3/92 | NT | 7.8% | coding (245/354 nt) | ychN | conserved hypothetical protein |
| ? | Exported | 825063 = | 59 (0.910) | coding (216/354 nt) | ychN | conserved hypothetical protein | |||||
| * | ? | Exported | 981368 = | 59 (0.840) | 6 (0.100) | 3/88 | NT | 9.8% | coding (326/533 nt) | ydfQ | predicted lysozyme |
| ? | Exported | 981396 = | 58 (0.930) | coding (298/533 nt) | ydfQ | predicted lysozyme | |||||
| * | ? | Exported | = 1230703 | 34 (0.480) | 3 (0.050) | 3/94 | NT | 8.2% | coding (2053/2061 nt) | ptrB | protease II |
| ? | Exported | = 1230732 | 35 (0.530) | coding (2024/2061 nt) | ptrB | protease II | |||||
| * | ? | Exported | 1637071 = | 60 (0.850) | 7 (0.110) | 3/92 | NT | 10.6% | intergenic (+95/‑444) | acrD/yffB | aminoglycoside/multidrug efflux system/conserved hypothetical protein |
| ? | Exported | 1637110 = | 63 (0.970) | intergenic (+134/‑405) | acrD/yffB | aminoglycoside/multidrug efflux system/conserved hypothetical protein | |||||
| * | ? | Exported | = 1826756 | 55 (0.780) | 18 (0.260) | 10/98 | NT | 22.2% | intergenic (‑433/‑2) | hydN/mutS | formate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit/methyl‑directed mismatch repair protein |
| ? | Exported | 2705183 = | 72 (1.040) | coding (1/837 nt) | dam | DNA adenine methylase | |||||
| * | ? | Exported | = 1936471 | 54 (0.760) | 5 (0.080) | 3/92 | NT | 9.6% | coding (904/1734 nt) | recJ | ssDNA exonuclease, 5' ‑‑> 3'‑specific |
| ? | Exported | = 1936485 | 44 (0.680) | coding (890/1734 nt) | recJ | ssDNA exonuclease, 5' ‑‑> 3'‑specific | |||||
| * | ? | Exported | 2118619 = | 75 (1.060) | 6 (0.090) | 4/92 | NT | 7.7% | coding (133/2037 nt) | yraM | conserved hypothetical protein |
| ? | Exported | 2118653 = | 74 (1.140) | coding (167/2037 nt) | yraM | conserved hypothetical protein | |||||
| * | ? | Exported | 2406673 = | 60 (0.850) | 4 (0.060) | 3/92 | NT | 6.4% | coding (788/2547 nt) | cyaA | adenylate cyclase |
| ? | Exported | 2406702 = | 61 (0.940) | coding (759/2547 nt) | cyaA | adenylate cyclase | |||||
| * | ? | Exported | = 2736154 | 33 (0.470) | 4 (0.060) | 3/88 | NT | 9.6% | coding (1298/2115 nt) | fusA | protein chain elongation factor EF‑G |
| ? | Exported | = 2736178 | 46 (0.740) | coding (1322/2115 nt) | fusA | protein chain elongation factor EF‑G | |||||
| * | ? | Exported | = 2738692 | 54 (0.760) | 7 (0.110) | 3/90 | NT | 13.4% | intergenic (+466/‑63) | tufA/rpsJ | protein chain elongation factor EF‑Tu/30S ribosomal subunit protein S10 |
| ? | Exported | = 2738700 | 42 (0.660) | intergenic (+474/‑55) | tufA/rpsJ | protein chain elongation factor EF‑Tu/30S ribosomal subunit protein S10 | |||||