mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 158,294 | G→A | T278I (ACC→ATC) | pcnB ← | poly(A) polymerase I |
| RA | 163,296 | (G)5→6 | coding (1192/2430 nt) | hrpB → | putative ATP‑dependent RNA helicase HrpB |
| RA | 167,697 | Δ1 bp | coding (214/2244 nt) | fhuA → | ferrichrome outer membrane transporter/phage receptor |
| RA | 273,130 | A→G | N95S (AAC→AGC) | ykfC → | CP4‑6 prophage; PF00078 domain‑containing protein YkfC |
| RA | 361,049 | A→G | D353G (GAC→GGC) | cynX → | cyanate transporter |
| JC | 380,020 | (G)10→7 | intergenic (‑139/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 400,314 | A→G | Y204H (TAC→CAC) | ddlA ← | D‑alanine‑‑D‑alanine ligase A |
| RA | 409,904 | T→C | D39G (GAC→GGC) | rdgC ← | nucleoid‑associated protein RdgC |
| RA | 416,819 | A→G | V45A (GTT→GCT) | sbcD ← | ATP dependent, structure specific DNA nuclease ‑ SbcD subunit |
| RA | 447,207 | C→T | A167T (GCT→ACT) | cyoE ← | heme O synthase |
| RA | 548,591 | C→T | L79L (CTG→TTG) | ylbE → | DUF1116 domain‑containing protein YlbE |
| RA | 551,696 | A→G | V300A (GTG→GCG) | purK ← | 5‑(carboxyamino)imidazole ribonucleotide synthase |
| RA | 580,132 | C→T | intergenic (+46/+119) | ybcW → / ← ylcI | DLP12 prophage; protein YbcW/DLP12 prophage; DUF3950 domain‑containing protein YlcI |
| RA | 768,735 | A→G | E253G (GAG→GGG) | mngB → | alpha‑mannosidase |
| RA | 807,114 | T→C | Q56Q (CAA→CAG) | ybhC ← | outer membrane lipoprotein YhbC |
| RA | 826,589 | T→C | T222A (ACC→GCC) | ybhS ← | putative ABC exporter membrane subunit YbhS |
| RA | 834,595 | C→T | P509L (CCT→CTT) | dinG → | ATP‑dependent DNA helicase DinG |
| RA | 837,442 | (A)8→7 | intergenic (+6/+223) | hcxB → / ← ybiJ | hydroxycarboxylate dehydrogenase B/DUF1471 domain‑containing protein YbiJ |
| RA | 841,961 | A→G | G32G (GGT→GGC) | mcbA ← | DUF1471 domain‑containing protein McbA |
| RA | 861,805 | A→G | C268R (TGT→CGT) | ybiW ← | putative pyruvate formate lyase |
| RA | 991,454 | C→T | A278V (GCC→GTC) | pepN → | aminopeptidase N |
| RA | 1,028,548 | G→A | D58D (GAC→GAT) | hspQ ← | heat shock protein, hemimethylated DNA‑binding protein |
| RA | 1,034,399 | C→T | S382S (AGC→AGT) | hyaB → | hydrogenase 1 large subunit |
| RA | 1,070,824 | C→T | P44P (CCG→CCA) | rutE ← | putative malonic semialdehyde reductase |
| RA | 1,072,231 | G→A | V211V (GTC→GTT) | rutB ← | peroxyureidoacrylate/ureidoacrylate amidohydrolase |
| RA | 1,134,942 | (G)5→4 | coding (214/783 nt) | flgG → | flagellar basal‑body rod protein FlgG |
| RA | 1,153,604 | G→A | R102Q (CGG→CAG) | pabC → | aminodeoxychorismate lyase |
| RA | 1,194,966 | G→T | intergenic (‑15/‑157) | rluE ← / → icd | 23S rRNA pseudouridine(2457) synthase/isocitrate dehydrogenase |
| RA | 1,249,503 | A→G | G85G (GGT→GGC) | dhaL ← | dihydroxyacetone kinase subunit L |
| RA | 1,296,886 | T→C | K412K (AAA→AAG) | adhE ← | aldehyde‑alcohol dehydrogenase |
| RA | 1,335,476 | A→G | intergenic (+18/‑96) | yciX → / → ymiC | uncharacterized protein YciX/protein YmiC |
| RA | 1,405,854 | G→A | intergenic (‑103/‑125) | mcaS ← / → smrA | small regulatory RNA McaS/DNA endonuclease SmrA |
| RA | 1,423,367 | C→T | pseudogene (23/300 nt) | rzpR → | Rac prophage; putative endopeptidase RzpR |
| RA | 1,597,313 | (C)7→8 | pseudogene (774/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,604,255 | G→A | G70D (GGC→GAC) | lsrD → | Autoinducer‑2 ABC transporter membrane subunit LsrD |
| RA | 1,637,726 | (T)8→7 | coding (57/174 nt) | gnsB ← | Qin prophage; protein GnsB |
| RA | 1,649,566 | C→T | intergenic (+132/‑43) | dicF → / → dicB | Qin prophage; small regulatory RNA DicF/Qin prophage; cell division inhibition protein DicB |
| RA | 1,728,736 | G→A | M130I (ATG→ATA) | rnt → | RNase T |
| RA | 1,754,134 | T→A | D115V (GAT→GTT) | ydhY ← | putative 4Fe‑4S ferredoxin‑type protein |
| RA | 1,768,441 | (G)6→7 | coding (245/3057 nt) | ydiJ ← | putative FAD‑linked oxidoreductase |
| RA | 1,782,477 | G→A | M361I (ATG→ATA) | ydiS → | putative oxidoreductase with FAD/NAD(P)‑binding domain |
| JC JC | 1,873,031 | IS1 (–) +9 bp | coding (991‑999/1491 nt) | dgcJ → | putative diguanylate cyclase DgcJ |
| RA | 2,000,791 | T→C | L78L (TTA→TTG) | fliZ ← | DNA‑binding transcriptional regulator FliZ |
| RA | 2,140,599 | G→A | G338G (GGC→GGT) | asmA ← | putative assembly protein AsmA |
| RA | 2,163,201 | T→C | V109A (GTG→GCG) | baeS → | sensory histidine kinase BaeS |
| RA | 2,294,136 | T→C | T257A (ACT→GCT) | ccmF ← | holocytochrome c synthetase membrane subunit CcmF |
| RA | 2,359,683 | G→A | S157L (TCA→TTA) | yfaV ← | putative transporter YfaV |
| RA | 2,405,816 | G→A | L276L (CTG→TTG) | lrhA ← | DNA‑binding transcriptional dual regulator LrhA |
| RA | 2,465,729 | G→A | V143V (GTG→GTA) | yfdC → | inner membrane protein YfdC |
| RA | 2,466,831 | T→C | I96T (ATT→ACT) | intS → | CPS‑53 (KpLE1) prophage; prophage CPS‑53 integrase |
| RA | 2,567,316 | G→A | G264G (GGC→GGT) | eutH ← | putative inner membrane protein |
| RA | 2,576,457 | C→T | D641N (GAC→AAC) | maeB ← | malate dehydrogenase |
| RA | 2,613,439 | G→A | E514K (GAA→AAA) | hyfR → | DNA‑binding transcriptional activator HyfR |
| RA | 2,626,182 | T→C | H356H (CAT→CAC) | ppx → | exopolyphosphatase |
| RA | 2,726,545 | (C)6→5 | noncoding (2640/2904 nt) | rrlG ← | 23S ribosomal RNA |
| RA | 2,729,487 | G→A | intergenic (‑43/+129) | gltW ← / ← rrsG | tRNA‑Glu/16S ribosomal RNA |
| RA | 2,744,132 | G→A | intergenic (+25/+51) | yfiB → / ← rplS | lipoprotein YfiB/50S ribosomal subunit protein L19 |
| RA | 2,794,762 | T→C | G170G (GGT→GGC) | gabP → | 4‑aminobutyrate:H(+) symporter |
| RA | 2,875,413 | T→C | T3A (ACC→GCC) | cysN ← | sulfate adenylyltransferase subunit 1 |
| RA | 2,880,042 | A→G | L116L (TTA→CTA) | casE ← | pre‑CRISPR RNA endonuclease |
| RA | 2,925,331 | G→A | intergenic (‑51/‑17) | syd ← / → queF | SecY‑interacting protein/7‑cyano‑7‑deazaguanine reductase |
| RA | 2,931,803 | T→C | V250A (GTA→GCA) | ygdG → | flap endonuclease |
| RA | 2,943,337 | A→G | M1M (ATG→GTG) † | csdA → | cysteine sulfinate desulfinase |
| RA | 2,968,626 | T→C | T118A (ACA→GCA) | rppH ← | RNA pyrophosphohydrolase |
| RA | 3,209,413 | (G)5→6 | coding (1390/1464 nt) | ttdT → | L‑tartrate:succinate antiporter |
| RA | 3,216,481 | (G)6→7 | coding (11/765 nt) | nfeF ← | NADPH‑dependent ferric chelate reductase |
| RA | 3,225,547 | G→A | G972D (GGC→GAC) | ebgA → | evolved beta‑D‑galactosidase subunit alpha |
| RA | 3,248,374 | T→C | V201A (GTG→GCG) | yqjA → | DedA family protein YqjA |
| RA | 3,305,029 | G→A | G263G (GGC→GGT) | mtr ← | tryptophan:H(+) symporter Mtr |
| RA | 3,433,495 | G→A | V22V (GTC→GTT) | smf ← | protein Smf |
| RA | 3,584,362 | A→G | intergenic (+53/‑42) | yrhA → / → yrhD | putative uncharacterized protein YrhA/uncharacterized protein YrhD |
| RA | 4,138,019 | C→T | M339I (ATG→ATA) | gldA ← | L‑1,2‑propanediol dehydrogenase/glycerol dehydrogenase |
| RA | 4,240,047 | A→G | R3R (CGT→CGC) | yjbT ← | PF17089 family protein YjbT |
| RA | 4,274,907 | A→G | G45G (GGT→GGC) | yjcB ← | uncharacterized protein YjcB |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,354,298 | A→G | C140C (TGT→TGC) | lysU ← | lysine‑‑tRNA ligase/Ap4A synthetase/Ap3A synthetase |
| RA | 4,441,588 | C→A | G197C (GGT→TGT) | msrA ← | methionine sulfoxide reductase A |
| RA | 4,445,655 | T→A | I515N (ATC→AAC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,545,025 | A→G | E241G (GAA→GGA) | fimC → | type 1 fimbriae periplasmic chaperone |
| RA | 4,562,313 | A→G | G121G (GGT→GGC) | yjiJ ← | putative transporter YjiJ |
| RA | 4,588,033 | C→T | R278H (CGC→CAC) | yjiA ← | P‑loop guanosine triphosphatase |
| RA | 4,594,249 | C→T | W158* (TGG→TGA) | lgoT ← | galactonate:H(+) symporter |
| RA | 4,606,330 | (G)8→10 | noncoding (72/87 nt) | leuQ ← | tRNA‑Leu |
| RA | 4,629,731 | C→T | A264A (GCG→GCA) | ettA ← | energy‑dependent translational throttle protein EttA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 361203 | 361922 | 720 | 170 [165] | [163] 168 | lacA | lacA |
| * | * | ÷ | NC_000913 | 2856990 | 2857095 | 106 | 167 [165] | [0] 275 | [mutS] | [mutS] |
| * | * | ÷ | NC_000913 | 3423682–3424234 | 3424614–3424238 | 5–933 | 167 [165] | [165] 169 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 70046 = | 291 (0.960) | 259 (0.880) | 132/188 | 0.7 | 64.8% | coding (3/1701 nt) | araB | ribulokinase |
| ? | NC_000913 | 2857096 = | 0 (0.000) | coding (4/2562 nt) | mutS | DNA mismatch repair protein MutS | |||||
| * | ? | NC_000913 | 1207790 = | 153 (0.500) | 162 (0.640) | 102/162 | 1.6 | 56.6% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 121 (0.480) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 2726540 = | 0 (0.000) | 201 (0.680) | 124/188 | 1.2 | 100% | noncoding (2645/2904 nt) | rrlG | 23S ribosomal RNA |
| ? | NC_000913 | 3946346 = | NA (NA) | noncoding (2643/2904 nt) | rrlC | 23S ribosomal RNA | |||||