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 49,736 A→T intergenic (+105/‑87) kefC → / → folA glutathione‑regulated potassium‑efflux system protein KefC/type 3 dihydrofolate reductase
RA 49,903 T→A D27E (GAT→GAA folA → type 3 dihydrofolate reductase
RA 50,280 T→C F153S (TTT→TCT)  folA → type 3 dihydrofolate reductase
RA 56,392 A→C Y240D (TAC→GAC)  lptD ← LPS assembly protein LptD
RA 108,362 A→G F242S (TTC→TCC)  zapD ← cell division protein ZapD
RA 115,488 T→C F90S (TTC→TCC)  ampD → 1,6‑anhydro‑N‑acetylmuramyl‑L‑alanine amidase AmpD
RA 115,628 A→C T137P (ACG→CCG)  ampD → 1,6‑anhydro‑N‑acetylmuramyl‑L‑alanine amidase AmpD
RA 130,698 A→T *866L (TAA→TTA)  acnB → bifunctional aconitate hydratase 2/2‑methylisocitrate dehydratase
RA 139,618 A→G E118G (GAA→GGA)  yadG → ABC transporter ATP‑binding protein
RA 209,716 T→C I300T (ATC→ACC)  tilS → tRNA lysidine(34) synthetase TilS
RA 221,335 T→C noncoding (1078/1542 nt) BW25113_RS01010 → 16S ribosomal RNA
RA 231,042 A→C G76G (GGT→GGG gloB ← hydroxyacylglutathione hydrolase
RA 232,840 T→A V96E (GTG→GAG)  dnaQ → DNA polymerase III subunit epsilon
RA 264,689 (A)5→4 intergenic (‑18/+311) ykfA ← / ← perR GTPase family protein/LysR substrate‑binding domain‑containing protein
RA 297,509 G→C G30G (GGC→GGG paoB ← aldehyde oxidoreductase FAD‑binding subunit PaoB
RA 322,687 A→G I91T (ATC→ACC)  betA ← choline dehydrogenase
RA 340,444 (A)5→4 coding (558/816 nt) BW25113_RS01680 → hypothetical protein
RA 354,025 T→C E126G (GAA→GGA)  cynR ← transcriptional regulator CynR
RA 385,080 A→C I35S (ATC→AGC)  hemB ← porphobilinogen synthase
RA 386,045 T→C pseudogene (339/1527 nt) BW25113_RS01915 → outer membrane autotransporter barrel domain‑containing protein
RA 444,519 G→A R527C (CGT→TGT)  cyoB ← cytochrome o ubiquinol oxidase subunit I
RA 463,972 A→G D45G (GAC→GGC)  decR → DNA‑binding transcriptional regulator DecR
RA 465,464 T→C S380P (TCG→CCG)  mdlA → SmdA family multidrug ABC transporter permease/ATP‑binding protein
RA 476,525 A→G intergenic (‑361/+185) tomB ← / ← acrB Hha toxicity modulator TomB/efflux RND transporter permease AcrB
RA 502,414 T→C D42G (GAT→GGT)  ybaK ← Cys‑tRNA(Pro)/Cys‑tRNA(Cys) deacylase YbaK
RA 508,601 (C)6→7 coding (570/1293 nt) ybaT → APC family permease
RA 510,152 Δ1 bp coding (164/459 nt) ybbJ ← NfeD family protein
RA 539,975 A→G D258D (GAT→GAC allC ← allantoate deiminase
RA 554,427 A→G intergenic (+217/‑3) fimA → / → fimC type 1 fimbrial major subunit FimA/type 1 fimbria chaperone FimC
RA 568,752 A→G G71G (GGA→GGG ybcO → DUF1364 domain‑containing protein
RA 579,943 (T)8→7 intergenic (+57/+193) appY → / ← ompT DNA‑binding transcriptional activator AppY/omptin family outer membrane protease OmpT
RA 592,895 A→C L103F (TTA→TTC cusF → Cu(+)/Ag(+) efflux RND transporter periplasmic metallochaperone CusF
RA 601,986 A→G F285S (TTC→TCC)  ybdK ← YbdK family carboxylate‑amine ligase
RA 609,731 A→G D40G (GAT→GGT)  entF → enterobactin non‑ribosomal peptide synthetase EntF
RA 661,892 A→C G594G (GGT→GGG mrdA ← peptidoglycan DD‑transpeptidase MrdA
RA 674,442 T→G T141P (ACT→CCT)  ybeT ← tetratricopeptide repeat protein
RA 802,549 T→G T63T (ACA→ACC ybhC ← putative acyl‑CoA thioester hydrolase
RA 874,237 C→T L14F (CTT→TTT)  yliI → aldose sugar dehydrogenase YliI
RA 885,317 T→C intergenic (‑42/‑228) ybjL ← / → ybjM aspartate:alanine antiporter/inner membrane protein YbjM
RA 886,189 A→G G7G (GGT→GGC grxA ← glutaredoxin 1
RA 915,296 C→G G202G (GGC→GGG macA → macrolide transporter subunit MacA
RA 950,036 (T)5→4 intergenic (‑114/+292) focA ← / ← ycaO formate transporter FocA/30S ribosomal protein S12 methylthiotransferase accessory factor YcaO
RA 951,809 T→G T94P (ACC→CCC)  ycaO ← 30S ribosomal protein S12 methylthiotransferase accessory factor YcaO
RA 979,260 T→C I52T (ATC→ACC)  gloC → hydroxyacylglutathione hydrolase GloC
RA 987,365 A→G N430D (AAT→GAT)  pepN → aminopeptidase N
RA 991,969 T→G L144F (TTA→TTC ssuA ← aliphatic sulfonate ABC transporter substrate‑binding protein SsuA
RA 1,021,663 (A)5→4 coding (1737/2055 nt) helD → DNA helicase IV
RA 1,054,234 A→G E232G (GAA→GGA)  torC → pentaheme c‑type cytochrome TorC
RA 1,060,988 (A)6→5 intergenic (+240/‑53) yccE → / → agp YccE family protein/bifunctional glucose‑1‑phosphatase/inositol phosphatase
RA 1,062,210 T→C G390G (GGT→GGC agp → bifunctional glucose‑1‑phosphatase/inositol phosphatase
RA 1,065,426 T→G T129P (ACC→CCC)  rutF ← pyrimidine utilization flavin reductase protein F
RA 1,076,727 (T)5→4 intergenic (+458/‑85) putP → / → BW25113_RS05295 sodium/proline symporter PutP/FTR1 family protein
RA 1,110,952 T→C intergenic (‑6/+166) mdtG ← / ← lpxL multidrug efflux MFS transporter MdtG/kdo(2)‑lipid IV(A) lauroyltransferase
RA 1,122,270 (A)6→5 coding (9/924 nt) yceM → Gfo/Idh/MocA family oxidoreductase
RA 1,153,703 A→T I127F (ATC→TTC)  ptsG → PTS glucose transporter subunit IIBC
RA 1,155,022 G→T T662T (ACC→ACA fhuE ← ferric‑rhodotorulic acid/ferric‑coprogen receptor FhuE
RA 1,167,328 T→C E698G (GAA→GGA)  mfd ← transcription‑repair coupling factor
RA 1,174,665 T→G L206W (TTG→TGG)  nagK → N‑acetylglucosamine kinase
RA 1,223,232 (A)8→7 coding (63/294 nt) BW25113_RS06140 → YcgL domain‑containing protein
RA 1,259,173 A→G T2A (ACC→GCC)  hemA → glutamyl‑tRNA reductase
RA 1,276,251 Δ1 bp coding (932/3744 nt) narG → nitrate reductase subunit alpha
RA 1,300,524 Δ1 bp coding (504/1005 nt) oppF → murein tripeptide/oligopeptide ABC transporter ATP‑binding protein OppF
RA 1,320,565 G→A Q521Q (CAG→CAA yciQ → DUF2207 domain‑containing protein
RA 1,325,886 T→C G194G (GGT→GGC topA → type I DNA topoisomerase
RA 1,331,016 A→G Y310C (TAT→TGT)  acnA → aconitate hydratase AcnA
RA 1,336,062 A→G intergenic (+78/‑116) lapB → / → pyrF lipopolysaccharide assembly protein LapB/orotidine‑5'‑phosphate decarboxylase
RA 1,363,696 T→C F16S (TTC→TCC)  pspD → phage shock protein PspD
RA 1,365,912 T→G R480R (CGT→CGG ycjM → glucosylglycerate phosphorylase
RA 1,392,826 T→C Q18Q (CAA→CAG uspE ← universal stress protein UspE
RA 1,394,163 G→A L111L (CTG→TTG)  ogt ← methylated‑DNA‑‑[protein]‑cysteine S‑methyltransferase
RA 1,394,663 T→C G456G (GGA→GGG abgT ← p‑aminobenzoyl‑glutamate transporter
RA 1,402,000 A→G I18T (ATC→ACC)  dgcM ← diguanylate cyclase DgcM
RA 1,417,788 (C)6→7 coding (69/120 nt) BW25113_RS26130 ← hypothetical protein
RA 1,423,602 T→C R99R (CGT→CGC stfR → prophage tail fiber N‑terminal domain‑containing protein
RA 1,431,536 T→C E1169G (GAA→GGA)  nifJ ← pyruvate:ferredoxin (flavodoxin) oxidoreductase
RA 1,434,377 A→G F222S (TTC→TCC)  nifJ ← pyruvate:ferredoxin (flavodoxin) oxidoreductase
RA 1,454,774 A→G D16G (GAT→GGT)  paaI → hydroxyphenylacetyl‑CoA thioesterase PaaI
RA 1,494,123 T→C E195G (GAA→GGA)  ydcK ← YdcK family protein
RA 1,499,566 A→G S258P (TCC→CCC)  ydcO ← BenE family transporter YdcO
RA 1,502,076 A→G N347D (AAC→GAC)  rlhA → 23S rRNA 5‑hydroxycytidine C2501 synthase
RA 1,503,965 T→C D67D (GAT→GAC hicB → type II toxin‑antitoxin system antitoxin HicB
RA 1,505,430 A→G K391E (AAA→GAA)  ydcR → PLP‑dependent aminotransferase family protein
RA 1,524,815 T→C intergenic (‑54/‑28) BW25113_RS25600 ← / → BW25113_RS07655 protein YncO/ISAs1 family transposase
RA 1,531,275 G→A L98L (CTG→TTG)  narW ← nitrate reductase molybdenum cofactor assembly chaperone
RA 1,547,935 A→G V54A (GTA→GCA)  adhP ← alcohol dehydrogenase AdhP
RA 1,558,439 A→G Y518H (TAT→CAT)  dosP ← oxygen‑sensing cyclic‑di‑GMP phosphodiesterase
RA 1,568,198 A→G F417S (TTC→TCC)  pqqL ← insulinase family protein
RA 1,573,157 A→T I148N (ATC→AAC)  yddA ← ABC transporter ATP‑binding protein/permease
RA 1,575,825 A→T D319E (GAT→GAA ydeN ← sulfatase
RA 1,576,388 A→G S132P (TCC→CCC)  ydeN ← sulfatase
RA 1,579,109 A→C G545G (GGT→GGG ydeP ← acid resistance putative oxidoreductase YdeP
RA 1,613,753 (A)6→5 coding (377/435 nt) marR → multiple antibiotic resistance transcriptional regulator MarR
RA 1,632,437 (T)7→6 intergenic (‑71/+8) BW25113_RS08135 ← / ← BW25113_RS25620 hypothetical protein/hypothetical protein
RA 1,634,151 Δ1 bp coding (164/534 nt) rrrQ ← lysozyme
RA 1,649,476 A→G intergenic (‑78/+128) rspA ← / ← ynfA starvation‑sensing protein RspA/YnfA family protein
RA 1,659,576 T→C F14S (TTC→TCC)  clcB → voltage‑gated ClC‑type chloride channel ClcB
RA 1,662,649 T→G H58P (CAC→CCC)  mlc ← DNA‑binding transcriptional repressor Mlc
RA 1,671,899 T→G T88P (ACG→CCG)  pntA ← Re/Si‑specific NAD(P)(+) transhydrogenase subunit alpha
RA 1,673,542 A→G K287E (AAG→GAG)  ydgH → DUF1471 family protein YdgH
RA 1,717,498 G→C G374A (GGC→GCC)  ydhK → FUSC family protein
RA 1,761,086 A→C R619R (CGT→CGG ydiJ ← FAD‑binding and (Fe‑S)‑binding domain‑containing protein
RA 1,782,276 T→G V192G (GTG→GGG)  ppsR → posphoenolpyruvate synthetase regulatory kinase/phosphorylase PpsR
RA 1,796,543 G→C G95G (GGC→GGG thrS ← threonine‑‑tRNA ligase
RA 1,803,201 A→G V97A (GTC→GCC)  yniB ← YniB family protein
RA 1,807,028 T→C E121G (GAA→GGA)  BW25113_RS09050 ← hypothetical protein
RA 1,812,807 (C)7→8 intergenic (‑50/+55) celF ← / ← chbR 6‑phospho‑beta‑glucosidase/transcriptional regulator ChbR
RA 1,818,956 T→G K80T (AAA→ACA)  ves ← environmental stress‑induced protein Ves
RA 1,838,813 T→C I106V (ATT→GTT)  ynjI ← DUF1266 domain‑containing protein
RA 1,840,928 T→C E97G (GAA→GGA)  topB ← DNA topoisomerase III
RA 1,848,011 T→C T76A (ACT→GCT)  ydjE ← MFS transporter
RA 1,854,126 T→C M121V (ATG→GTG)  ydjK ← MFS transporter
RA 1,869,539 G→C P99A (CCG→GCG)  nimR ← DNA‑binding transcriptional regulator NimR
RA 1,877,816 T→C pseudogene (408/1482 nt) yeaV → BCCT family transporter YeaV
RA 1,897,230 A→G D309G (GAT→GGT)  manX → PTS mannose transporter subunit IIAB
RA 1,900,885 A→G S145P (TCC→CCC)  rlmA ← 23S rRNA (guanine(745)‑N(1))‑methyltransferase
RA 1,903,061 A→T intergenic (‑38/‑121) mgrB ← / → yobH PhoP/PhoQ regulator MgrB/YobH family protein
RA 1,927,010 T→C K2E (AAA→GAA)  kdgA ← bifunctional 4‑hydroxy‑2‑oxoglutarate aldolase/2‑dehydro‑3‑deoxy‑phosphogluconate aldolase
RA 1,934,547 T→C intergenic (‑97/+23) lpxM ← / ← mepM lauroyl‑Kdo(2)‑lipid IV(A) myristoyltransferase/murein DD‑endopeptidase MepM
RA 1,941,604 A→C G10G (GGT→GGG ruvC ← crossover junction endodeoxyribonuclease RuvC
RA 1,961,177 C→G A40P (GCC→CCC)  cheZ ← protein phosphatase CheZ
RA 1,965,782 T→G E389D (GAA→GAC tar ← methyl‑accepting chemotaxis protein II
RA 1,972,691 A→G intergenic (‑237/‑543) flhD ← / → uspC flagellar transcriptional regulator FlhD/universal stress protein UspC
RA 1,980,420 A→G G5G (GGA→GGG ftnB → non‑heme ferritin‑like protein
RA 2,003,480 T→C F60S (TTC→TCC)  yedK → SOS response‑associated peptidase
RA 2,038,183 (T)5→4 intergenic (+78/‑236) BW25113_RS10330 → / → yeeJ tRNA‑Asn/inverse autotransporter adhesin YeeJ
RA 2,057,664 T→C G95G (GGA→GGG cobT ← nicotinate‑nucleotide‑‑dimethylbenzimidazole phosphoribosyltransferase
RA 2,061,342 T→A intergenic (‑576/‑774) BW25113_RS10415 ← / → BW25113_RS24005 IS5‑like element IS5 family transposase/TonB‑dependent receptor plug domain‑containing protein
RA 2,064,259 T→G V93G (GTG→GGG)  BW25113_RS10440 → GTPase family protein
RA 2,102,646 T→C G140G (GGA→GGG wzx ← O16 family O‑antigen flippase
RA 2,131,004 A→G intergenic (‑280/‑379) wza ← / → yegH polysaccharide export protein Wza/TerC family protein
RA 2,174,381 T→G C270G (TGC→GGC)  yegU → ADP‑ribosylglycohydrolase family protein
RA 2,176,805 T→G D109A (GAC→GCC)  yegX ← glycoside hydrolase family 25 protein
RA 2,189,312 A→G T512A (ACC→GCC)  metG → methionine‑‑tRNA ligase
RA 2,202,171 G→C W242C (TGG→TGC yehP → VWA domain‑containing protein
RA 2,220,044 A→G S236P (TCG→CCG)  yohF ← SDR family oxidoreductase
RA 2,229,956 A→G K405E (AAA→GAA)  preA → NAD‑dependent dihydropyrimidine dehydrogenase subunit PreA
RA 2,283,874 Δ1 bp intergenic (‑350/‑105) BW25113_RS11435 ← / → narP IS5‑like element IS5 family transposase/nitrate/nitrite response regulator protein NarP
RA 2,284,519 T→C S181P (TCC→CCC)  narP → nitrate/nitrite response regulator protein NarP
RA 2,345,414 T→G H147P (CAC→CCC)  glpT ← glycerol‑3‑phosphate transporter
RA 2,358,446 Δ1 bp coding (414/426 nt) nudI → nucleoside triphosphatase NudI
MC JC 2,399,465 Δ7 bp coding (650‑656/939 nt) lrhA ← transcriptional regulator LrhA
RA 2,410,868 A→T G103G (GGA→GGT yfcC → putative basic amino acid antiporter YfcC
RA 2,425,778 T→C E215G (GAA→GGA)  folC ← bifunctional tetrahydrofolate synthase/dihydrofolate synthase
RA 2,434,529 A→C F186V (TTT→GTT)  fabB ← beta‑ketoacyl‑ACP synthase I
RA 2,439,101 T→C K255E (AAG→GAG)  mepA ← penicillin‑insensitive murein endopeptidase
RA 2,505,777 T→C I137V (ATC→GTC)  mntH ← Nramp family divalent metal transporter
RA 2,526,050 A→G T95A (ACC→GCC)  cysK → cysteine synthase A
RA 2,536,106 T→C E261G (GAA→GGA)  cysP ← thiosulfate/sulfate ABC transporter substrate‑binding protein CysP
RA 2,554,121 A→C N169T (AAC→ACC)  BW25113_RS12740 → hypothetical protein
RA 2,591,366 C→T D287N (GAC→AAC)  bamC ← outer membrane protein assembly factor BamC
RA 2,661,508 T→G T250P (ACC→CCC)  hcaR ← DNA‑binding transcriptional regulator HcaR
RA 2,670,359 T→C G454G (GGA→GGG yphE ← sugar ABC transporter ATP‑binding protein
RA 2,678,723 A→C G48G (GGT→GGG glyA ← serine hydroxymethyltransferase
RA 2,726,562 (T)5→4 coding (971/2574 nt) clpB ← ATP‑dependent chaperone ClpB
RA 2,739,096 T→C E61G (GAA→GGA)  rimM ← ribosome maturation factor RimM
RA 2,751,237 A→G V241V (GTT→GTC BW25113_RS13685 ← hypothetical protein
RA 2,753,169 T→C S276P (TCA→CCA)  yfjI → YfjI family protein
RA 2,759,232 (G)6→7 intergenic (‑97/‑45) yfjM ← / → rnlA DUF1524 domain‑containing protein/type II toxin‑antitoxin system toxin mRNA endoribonuclease RnlA
RA 2,778,934 (T)6→5 intergenic (‑564/+187) BW25113_RS25705 ← / ← BW25113_RS13825 DUF5507 domain‑containing protein/tRNA‑Ile
RA 2,797,377 (T)5→4 coding (517/960 nt) nrdF → class 1b ribonucleoside‑diphosphate reductase subunit beta
RA 2,801,112 A→C T208P (ACC→CCC)  proX → glycine betaine/L‑proline ABC transporter substrate‑binding protein ProX
RA 2,814,267 A→G A368A (GCT→GCC alaS ← alanine‑‑tRNA ligase
RA 2,818,451 T→C E162G (GAA→GGA)  mltB ← lytic murein transglycosylase B
RA 2,819,095 T→C intergenic (‑160/‑96) mltB ← / → srlA lytic murein transglycosylase B/PTS glucitol/sorbitol transporter subunit IIC
RA 2,833,262 T→G V127G (GTC→GGC)  ascF → PTS cellobiose/arbutin/salicin transporter subunit IIBC
RA 2,849,315 A→C Y540S (TAC→TCC)  flhA → formate hydrogenlyase transcriptional activator FlhA
RA 2,849,816 T→C E117G (GAA→GGA)  ygbA ← nitrous oxide‑stimulated promoter family protein
RA 2,859,998 T→C I305V (ATT→GTT)  rpoS ← RNA polymerase sigma factor RpoS
RA 2,882,413 A→C V349G (GTT→GGT)  cysI ← assimilatory sulfite reductase (NADPH) hemoprotein subunit
RA 2,888,711 A→G V143A (GTC→GCC)  ygcQ ← electron transfer flavoprotein subunit alpha/FixB family protein
RA 2,982,555 T→C F232S (TTC→TCC)  yqeI → transcriptional regulator
RA 2,995,567 A→G T635A (ACC→GCC)  xdhA → xanthine dehydrogenase molybdenum‑binding subunit XdhA
RA 3,011,010 A→G E531G (GAA→GGA)  ygfK → putative selenate reductase subunit YgfK
RA 3,098,336 Δ1 bp coding (545/1080 nt) mltC → membrane‑bound lytic murein transglycosylase MltC
RA 3,103,871 (A)7→6 intergenic (+71/+78) BW25113_RS15410 → / ← yghD tRNA‑Phe/GspM family type II secretion system protein YghD
RA 3,113,649 T→G K330N (AAA→AAC glcA ← glycolate permease GlcA
RA 3,179,271 G→A A167T (GCC→ACC)  ygiL → fimbrial‑like protein
RA 3,273,721 A→G E49G (GAA→GGA)  agaV → PTS N‑acetylgalactosamine transporter subunit IIB
RA 3,458,386 A→G E369G (GAA→GGA)  gspL → type II secretion system protein GspL
RA 3,475,701 T→C S352P (TCG→CCG)  yheS → ABC transporter ATP‑binding protein
RA 3,535,339 T→C F525S (TTC→TCC)  feoB → Fe(2+) transporter permease subunit FeoB
RA 3,576,634 A→G R79R (CGA→CGG BW25113_RS17825 → YrhA family protein
RA 3,579,168 T→C E339G (GAA→GGA)  ggt ← gamma‑glutamyltransferase
RA 3,717,969 T→C E237G (GAA→GGA)  glyQ ← glycine‑‑tRNA ligase subunit alpha
RA 3,728,024 A→C S315S (TCA→TCC xylH → xylose ABC transporter permease XylH
RA 3,771,044 A→G K96E (AAA→GAA)  lldP → L‑lactate permease
RA 3,785,687 G→C G75G (GGC→GGG kbl ← glycine C‑acetyltransferase
RA 3,786,467 T→C I193V (ATT→GTT)  yibB ← protein YibB
RA 3,786,991 T→C D18G (GAT→GGT)  yibB ← protein YibB
RA 3,791,182 A→C Y292S (TAC→TCC)  waaL → O‑antigen ligase
RA 3,840,691 T→G N432H (AAC→CAC)  uhpC ← MFS transporter family glucose‑6‑phosphate receptor UhpC
RA 3,848,051 T→G F257C (TTT→TGT)  emrD → multidrug efflux MFS transporter EmrD
RA 3,852,078 T→G T467P (ACG→CCG)  yidK ← solute:sodium symporter family transporter
RA 3,896,621 A→G D147D (GAT→GAC bglB ← 6‑phospho‑beta‑glucosidase BglB
RA 3,898,828 (T)5→4 coding (130/1878 nt) bglF ← PTS beta‑glucoside transporter subunit IIABC
RA 3,901,121 A→G D202D (GAT→GAC pstB ← phosphate ABC transporter ATP‑binding protein PstB
RA 3,931,448 G→T L265F (TTG→TTT rbsK → ribokinase
RA 3,934,995 +C intergenic (‑308/‑173) yieP ← / → BW25113_RS19520 FadR/GntR family transcriptional regulator/16S ribosomal RNA
RA 4,034,572 T→G Q74H (CAA→CAC mobB ← molybdopterin‑guanine dinucleotide biosynthesis protein MobB
RA 4,057,873 C→G W418C (TGG→TGC yihO ← MFS transporter
RA 4,064,564 A→G Y185H (TAT→CAT)  yihS ← sulfoquinovose isomerase
RA 4,073,163 A→T D26V (GAT→GTT)  BW25113_RS20185 → hypothetical protein
RA 4,084,653 A→G G358G (GGT→GGC frvB ← PTS fructose‑like transporter subunit IIBC
RA 4,108,830 A→G H143H (CAT→CAC rraA ← ribonuclease E activity regulator RraA
RA 4,117,071 T→C F44S (TTC→TCC)  rpmE → 50S ribosomal protein L31
RA 4,153,816 T→C S84P (TCA→CCA)  btuB → TonB‑dependent vitamin B12 receptor BtuB
RA 4,180,586 (A)7→6 intergenic (+333/+77) yjaZ → / ← thiH heat‑shock protein C/2‑iminoacetate synthase ThiH
RA 4,211,170 (T)8→7 coding (1246/2187 nt) espL4 ← type III secretion system effector EspL4
RA 4,215,724 T→G W657G (TGG→GGG)  metH → methionine synthase
RA 4,306,692 A→T I115N (ATC→AAC)  phnM ← alpha‑D‑ribose 1‑methylphosphonate 5‑triphosphate diphosphatase
RA 4,350,381 G→C G457G (GGC→GGG cadC ← lysine decarboxylation/transport transcriptional activator CadC
RA 4,367,563 T→C intergenic (‑24/+65) blc ← / ← ampC lipocalin Blc/BlaEC family class C beta‑lactamase
RA 4,494,539 T→C F222S (TTC→TCC)  nanX → MFS transporter
RA 4,527,151 T→C Q87Q (CAA→CAG nanS ← 9‑O‑acetyl‑N‑acetylneuraminic acid deacetylase
RA 4,543,103 A→G E129G (GAA→GGA)  uxuB → fructuronate reductase
RA 4,593,447 T→C S52P (TCC→CCC)  yjjQ → response regulator transcription factor
RA 4,613,222 C→G R238P (CGC→CCC)  lplA ← lipoate‑‑protein ligase LplA

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NZ_CP009273 356981 357567 587 2 [0] [0] 2 lacA galactoside O‑acetyltransferase
* * ÷ NZ_CP009273 428494 428520 27 2 [1] [1] 3 nrdR transcriptional regulator NrdR
* * ÷ NZ_CP009273 716517 716538 22 3 [1] [1] 2 kdpE two‑component system response regulator KdpE
* * ÷ NZ_CP009273 902998 903048 51 2 [1] [1] 2 ybjT SDR family oxidoreductase
* * ÷ NZ_CP009273 982775 982822 48 2 [1] [1] 2 ompF/asnS porin OmpF/asparagine‑‑tRNA ligase
* * ÷ NZ_CP009273 1025188 1025213 26 2 [1] [1] 2 rlmI 23S rRNA (cytosine(1962)‑C(5))‑methyltransferase RlmI
* * ÷ NZ_CP009273 1037814 1037867 54 2 [1] [1] 2 etk tyrosine‑protein kinase
* * ÷ NZ_CP009273 1172280 1172325 46 3 [1] [1] 3 lolD lipoprotein‑releasing ABC transporter ATP‑binding protein LolD
* * ÷ NZ_CP009273 1207567 1207581 15 2 [0] [0] 2 iraM/BW25113_RS25985 anti‑adapter protein IraM/protein YmgK
* * ÷ NZ_CP009273 1213547 1213567 21 3 [1] [1] 2 pdeG cyclic diguanylate phosphodiesterase
* * ÷ NZ_CP009273 1267287 1267301 15 2 [0] [1] 2 chaA sodium‑potassium/proton antiporter ChaA
* * ÷ NZ_CP009273 1272823 1272849 27 2 [1] [1] 2 narX nitrate/nitrite two‑component system sensor histidine kinase NarX
* * ÷ NZ_CP009273 1332459 1332492 34 2 [1] [1] 2 acnA aconitate hydratase AcnA
* * ÷ NZ_CP009273 1527529 1527547 19 3 [1] [1] 2 [pptA]–[yddH] [pptA],[yddH]
* * ÷ NZ_CP009273 1632883 1632921 39 2 [1] [1] 2 cspI cold shock protein CspI
* * ÷ NZ_CP009273 2097822 2097850 29 2 [1] [0] 2 wbbK glycosyltransferase family 1 protein
* * ÷ NZ_CP009273 2301174 2301213 40 2 [1] [0] 3 yojI microcin J25 efflux ABC transporter YojI
* * ÷ NZ_CP009273 2463656 2463665 10 2 [0] [1] 2 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 3247141 3247151 11 3 [1] [1] 2 yhaJ DNA‑binding transcriptional regulator YhaJ
* * ÷ NZ_CP009273 4225629 4225666 38 2 [1] [0] 2 pgi/yjbE glucose‑6‑phosphate isomerase/exopolysaccharide production protein YjbE

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 360104 =NA (NA)21 (1.230) 13/170 0.3 44.7% intergenic (‑35/+251) lacZ/BW25113_RS23320 beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
?NZ_CP009273 = 360286 26 (1.520)intergenic (‑217/+69) lacZ/BW25113_RS23320 beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
* ? NZ_CP009273 1203246 =6 (0.350)7 (0.500) 7/138 0.5 70.5% coding (290/630 nt) BW25113_RS05990 hypothetical protein
?NZ_CP009273 1205075 = 1 (0.070)coding (40/540 nt) BW25113_RS06005 phage tail protein
* ? NZ_CP009273 = 19727511 (0.060)18 (1.050) 12/170 0.3 94.7% intergenic (‑297/‑483) flhD/uspC flagellar transcriptional regulator FlhD/universal stress protein UspC
?NZ_CP009273 = 2283592 NA (NA)intergenic (‑68/‑387) BW25113_RS11435/narP IS5‑like element IS5 family transposase/nitrate/nitrite response regulator protein NarP