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 31,404 G→A L196L (CTG→CTA)  carB → carbamoyl phosphate synthetase subunit beta
RA 53,858 A→G V282A (GTG→GCG)  surA ← peptidyl‑prolyl cis‑trans isomerase SurA
RA 63,566 G→A P739S (CCG→TCG)  polB ← DNA polymerase II
RA 160,637 +C intergenic (‑33/+145) dksA ← / ← sfsA RNA polymerase‑binding transcription factor DksA/putative DNA‑binding transcriptional regulator of maltose metabolism
RA 206,530 A→G M469V (ATG→GTG)  dnaE → DNA polymerase III subunit alpha
RA 228,763 C→T noncoding (8/120 nt) rrfH → 5S ribosomal RNA
MC JC 257,908 Δ776 bp insB9–[crl] insB9, insA9, [crl]
RA 308,054 (C)7→8 coding (1279/2526 nt) ecpC ← putative fimbrial usher protein EcpC
RA 343,463 G→A A194T (GCC→ACC)  yahK → aldehyde reductase, NADPH‑dependent
RA 380,022 (G)10→9 intergenic (‑141/+47) frmR ← / ← yaiO DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO
RA 455,437 A→G D102G (GAC→GGC)  tig → trigger factor
RA 466,933 T→C Y127C (TAC→TGC)  ybaE ← putative protein YbaE
RA 474,489 Δ1 bp coding (673/861 nt) tesB ← acyl‑CoA thioesterase II
RA 510,590 A→G W264R (TGG→CGG)  copA ← Cu(+) exporting P‑type ATPase
RA 522,308 A→G Q631Q (CAA→CAG)  ybbP → putative ABC transporter membrane subunit YbbP
RA 527,577 T→C intergenic (+36/‑4) rhsD → / → ybbC protein RhsD/PF15631 family protein YbbC
RA 528,234 C→T pseudogene (286/711 nt) ylbH → putative RHS domain‑containing protein YlbH
RA 547,554 C→T A292V (GCG→GTG)  fdrA → putative acyl‑CoA synthetase FdrA
RA 554,220 T→C N73S (AAC→AGC)  ppiB ← peptidyl‑prolyl cis‑trans isomerase B
RA 606,120 (G)5→6 coding (80/249 nt) ybdJ ← DUF1158 domain‑containing protein YbdJ
RA 654,886 C→T A361A (GCG→GCA)  dcuC ← anaerobic C4‑dicarboxylate transporter DcuC
RA 717,125 (G)6→7 coding (1141/1320 nt) potE ← putrescine:H(+) symporter/putrescine:ornithine antiporter PotE
RA 721,645 T→G E30A (GAG→GCG)  kdpE ← DNA‑binding transcriptional activator KdpE
RA 751,514 (A)5→4 coding (656/2448 nt) ybgQ ← putative fimbrial usher protein YbgQ
RA 751,737 (G)6→7 coding (433/2448 nt) ybgQ ← putative fimbrial usher protein YbgQ
RA 766,957 (G)6→7 coding (974/1977 nt) mngA → 2‑O‑alpha‑mannosyl‑D‑glycerate specific PTS enzyme II
RA 769,676 T→C Y567H (TAT→CAT)  mngB → alpha‑mannosidase
RA 846,947 A→G F58S (TTT→TCT)  glnP ← L‑glutamine ABC transporter membrane subunit
RA 848,854 C→T D20N (GAT→AAT)  dps ← stationary phase nucleoid protein that sequesters iron and protects DNA from damage
RA 868,414 G→C A299P (GCC→CCC)  gsiA → glutathione ABC transporter ATP binding subunit GsiA
RA 885,544 A→G L196L (CTT→CTC)  ybjI ← 5‑amino‑6‑(5‑phospho‑D‑ribitylamino)uracil phosphatase
RA 889,923 A→G intergenic (‑104/‑166) ybjL ← / → ybjM putative transport protein YbjL/putative inner membrane protein
RA 925,623 A→G intergenic (+83/+261) clpA → / ← serW ATP‑dependent Clp protease ATP‑binding subunit ClpA/tRNA‑Ser
RA 932,340 (A)8→7 intergenic (‑290/‑255) trxB ← / → lrp thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp
RA 935,179 A→G A652A (GCA→GCG)  ftsK → cell division DNA translocase FtsK
RA 964,250 G→A intergenic (+138/‑70) ihfB → / → ycaI integration host factor subunit beta/conserved inner membrane protein YcaI
RA 1,000,908 A→G N565D (AAC→GAC)  elfC → putative fimbrial usher protein ElfC
RA 1,004,972 Δ1 bp coding (205/1011 nt) pyrD → dihydroorotate dehydrogenase, type 2
RA 1,010,898 C→T A312V (GCC→GTC)  uup → ATP‑binding protein with possible role in replication
RA 1,018,176 G→A L42L (CTG→TTG)  ycbZ ← putative ATP‑dependent protease YcbZ
RA 1,019,853 G→C N67K (AAC→AAG)  ompA ← outer membrane porin A
RA 1,029,953 A→G V6A (GTG→GCG)  rlmI ← 23S rRNA m(5)C1962 methyltransferase
RA 1,143,140 T→C T410A (ACT→GCT)  rne ← ribonuclease E
RA 1,159,950 A→G G534G (GGT→GGC)  fhuE ← ferric coprogen/ferric rhodotorulic acid outer membrane transporter
RA 1,160,848 A→G L235P (CTG→CCG)  fhuE ← ferric coprogen/ferric rhodotorulic acid outer membrane transporter
RA 1,161,362 A→G S64P (TCT→CCT)  fhuE ← ferric coprogen/ferric rhodotorulic acid outer membrane transporter
RA 1,183,673 A→G L258L (TTG→CTG)  potB ← spermidine preferential ABC transporter membrane subunit PotB
RA 1,191,945 T→C G14G (GGA→GGG)  purB ← adenylosuccinate lyase
RA 1,196,723 A→G intergenic (+350/+144) icd → / ← ymfD isocitrate dehydrogenase/e14 prophage; putative SAM‑dependent methyltransferase
RA 1,220,971 G→A pseudogene (1371/2648 nt) ycgH → putative transporter component, N‑terminal fragment
RA 1,257,583 A→G V77A (GTA→GCA)  ychF ← redox‑responsive ATPase YchF
RA 1,266,397 G→A A102T (GCA→ACA)  prmC → protein‑(glutamine‑N(5)) methyltransferase
RA 1,269,170 A→G *36Q (TAA→CAA)  ldrA ← small toxic polypeptide LdrA
RA 1,269,705 A→G *36Q (TAA→CAA)  ldrB ← small toxic polypeptide LdrB
RA 1,280,243 C→T A127V (GCG→GTG)  narG → nitrate reductase A subunit alpha
RA 1,280,714 A→G D284G (GAC→GGC)  narG → nitrate reductase A subunit alpha
MC JC 1,299,499 Δ1,199 bp insH21 insH21
RA 1,339,802 C→T A158V (GCC→GTC)  pgpB → phosphatidylglycerophosphatase B
RA 1,351,196 (G)7→6 intergenic (‑157/+211) fabI ← / ← ycjD enoyl‑[acyl‑carrier‑protein] reductase/DUF559 domain‑containing protein YcjD
RA 1,370,044 (T)9→8 intergenic (+41/‑172) pspE → / → ycjM thiosulfate sulfurtransferase PspE/glucosylglycerate phosphorylase
RA 1,377,092 A→G E87E (GAA→GAG)  ycjS → putative oxidoreductase YcjS
RA 1,390,763 G→A R34C (CGT→TGT)  ymjC ← putative uncharacterized protein YmjC
RA 1,419,486 G→A intergenic (‑30/+279) ydaG ← / ← racR Rac prophage; uncharacterized protein YdaG/Rac prophage; DNA‑binding transcriptional repressor RacR
JC JC 1,470,429 IS5 (+) +4 bp coding (1072‑1075/1152 nt) insI‑2 → IS30 transposase
RA 1,508,902 A→G S55P (TCG→CCG)  yncJ ← protein YncJ
RA 1,541,351 C→T E414K (GAA→AAA)  narZ ← nitrate reductase Z subunit alpha
RA 1,556,491 T→C intergenic (‑211/‑134) bdm ← / → osmC biofilm‑dependent modulation protein/osmotically inducible peroxiredoxin
RA 1,594,256 (C)8→9 pseudogene (3831/5422 nt) yneO ← AIDA‑I family autotransporter YneO
RA 1,624,072 C→T intergenic (‑222/+33) dgcZ ← / ← ydeI diguanylate cyclase DgcZ/BOF family protein YdeI
RA 1,634,642 C→T G82S (GGC→AGC)  tfaQ ← Qin prophage; putative tail fiber assembly protein TfaQ
RA 1,682,766 A→G D203G (GAC→GGC)  rstA → DNA‑binding transcriptional regulator RstA
RA 1,685,542 (C)6→5 coding (1047/1404 nt) fumC ← fumarase C
RA 1,714,949 A→G V191V (GTA→GTG)  gstA → glutathione S‑transferase GstA
RA 1,717,126 G→A P33S (CCG→TCG)  tyrS ← tyrosine‑‑tRNA ligase
RA 1,755,350 T→C intergenic (‑209/‑348) fumD ← / → pykF fumarase D/pyruvate kinase I
RA 1,796,199 T→C A582A (GCA→GCG)  pheT ← phenylalanine‑‑tRNA ligase subunit beta
RA 1,873,384 A→G K448K (AAA→AAG)  dgcJ → putative diguanylate cyclase DgcJ
JC JC 1,879,829 Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp coding (115‑120/360 nt) yeaR ← DUF1971 domain‑containing protein YeaR
RA 1,943,321 T→C R220R (CGT→CGC)  znuC → Zn(2(+)) ABC transporter ATP binding subunit
MC JC 1,978,503 Δ776 bp insB‑5–insA‑5 insB‑5, insA‑5
RA 2,002,039 T→C intergenic (‑250/+71) fliA ← / ← fliC RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein
RA 2,007,555 A→G E467G (GAG→GGG)  amyA → alpha‑amylase
RA 2,034,473 C→T pseudogene (423/1193 nt) yedS → putative outer membrane protein YedS, N‑terminal fragment
RA 2,078,942 T→C intergenic (+11/+90) yoeF → / ← yeeX CP4‑44 prophage; putative uncharacterized protein YoeF/DUF496 domain‑containing protein YeeX
RA 2,090,754 T→C I188T (ATC→ACC)  hisG → ATP phosphoribosyltransferase
RA 2,111,535 T→C I148V (ATT→GTT)  rfbD ← dTDP‑4‑dehydrorhamnose reductase
RA 2,114,013 G→A G105G (GGC→GGT)  galF ← UTP:glucose‑1‑phosphate uridylyltransferase, low activity
RA 2,139,829 T→C N595S (AAT→AGT)  asmA ← putative assembly protein AsmA
RA 2,148,330 T→C G219G (GGT→GGC)  yegD → HSP70 family protein YegD
RA 2,151,145 T→C intergenic (‑160/‑40) yegI ← / → yegJ protein kinase YegI/DUF2314 domain‑containing protein YegJ
RA 2,173,363 Δ2 bp pseudogene (915‑916/1358 nt) gatC ← galactitol‑specific PTS enzyme IIC component
RA 2,190,478 C→T E145K (GAA→AAA)  yehB ← putative fimbrial usher protein YehB
RA 2,197,062 T→C L197L (TTA→CTA)  yehF → putative protein YehF
RA 2,210,908 G→A W603* (TGG→TGA)  yehQ → SWIM zinc finger domains‑containing protein YehQ
RA 2,227,037 Δ1 bp coding (234/762 nt) yohF ← putative oxidoreductase with NAD(P)‑binding Rossmann‑fold domain
RA 2,227,340 (C)6→7 pseudogene (1419/1436 nt) mdtQ ← putative multidrug resistance outer membrane protein MdtQ
RA 2,259,392 T→C intergenic (‑96/+327) psuK ← / ← fruA putative pseudouridine kinase/fructose‑specific PTS multiphosphoryl transfer protein FruA
RA 2,269,260 T→C V136A (GTT→GCT)  lpxT → Kdo2‑lipid A phosphotransferase
RA 2,297,114 (C)7→8 coding (531/624 nt) ccmA ← heme trafficking system ATP‑binding protein
RA 2,336,768 T→C intergenic (‑124/+25) yfaA ← / ← gyrA DUF2138 domain‑containing protein YfaA/DNA gyrase subunit A
RA 2,339,206 T→C D72G (GAC→GGC)  gyrA ← DNA gyrase subunit A
RA 2,360,192 A→G intergenic (‑40/+17) yfaV ← / ← rhmD putative transporter YfaV/L‑rhamnonate dehydratase
RA 2,416,753 T→C R669R (CGT→CGC)  pta → phosphate acetyltransferase
RA 2,437,568 A→G V95A (GTG→GCG)  pdxB ← erythronate‑4‑phosphate dehydrogenase
RA 2,446,579 T→C T299A (ACC→GCC)  aroC ← chorismate synthase
RA 2,450,334 G→A P86L (CCG→CTG)  yfcP ← putative fimbrial protein YfcP
RA 2,462,889 (C)9→10 intergenic (+243/‑123) fadL → / → yfdF long‑chain fatty acid outer membrane channel/bacteriophage T2 receptor/protein YfdF
RA 2,492,417 T→C T280A (ACC→GCC)  frc ← formyl‑CoA transferase
RA 2,513,460 T→C V140A (GTC→GCC)  nupC → nucleoside:H(+) symporter NupC
RA 2,527,823 T→C V293A (GTG→GCG)  yfeH → putative solute:Na(+) symporter
RA 2,552,783 T→C G144G (GGT→GGC)  amiA → N‑acetylmuramoyl‑L‑alanine amidase A
RA 2,660,519 A→G V338A (GTG→GCG)  iscS ← cysteine desulfurase
RA 2,762,513 A→G V343A (GTC→GCC)  abpB ← CP4‑57 prophage; putative helicase YfjK
RA 2,811,134 A→G H122R (CAC→CGC)  mprA → DNA‑binding transcriptional repressor MprA
MC JC 2,857,096 Δ2,538 bp coding (4‑2541/2562 nt) mutS → DNA mismatch repair protein MutS
RA 2,870,137 T→C T46T (ACA→ACG)  umpG ← broad specificity 5'(3')‑nucleotidase and polyphosphatase
RA 2,870,797 T→C S170G (AGC→GGC)  truD ← tRNA pseudouridine(13) synthase
RA 2,927,705 T→C intergenic (+33/‑524) ppnN → / → sdaC nucleotide 5'‑monophosphate nucleosidase/serine:H(+) symporter SdaC
RA 2,949,993 (T)5→6 coding (752/1332 nt) argA → N‑acetylglutamate synthase
RA 2,962,491 (C)5→6 coding (274/324 nt) ppdC ← putative YgdA
RA 2,982,448 T→C intergenic (‑266/+49) araE ← / ← kduD arabinose:H(+) symporter/putative 2‑keto‑3‑deoxy‑D‑gluconate dehydrogenase
RA 2,988,500 G→A intergenic (+332/‑2) yqeH → / → yqeI putative LuxR family transcriptional regulator YqeH/putative transcriptional regulator YqeI
RA 3,020,551 A→T Q4H (CAA→CAT)  ygfM → putative oxidoreductase
RA 3,068,157 T→C intergenic (‑77/+16) yggE ← / ← argO uncharacterized protein YggE/L‑arginine exporter
RA 3,078,501 (T)5→6 coding (359/1389 nt) cmtA ← mannitol‑specific PTS enzyme IICB component CmtA
RA 3,100,292 T→C D146G (GAC→GGC)  ansB ← L‑asparaginase 2
RA 3,101,039 (C)7→8 coding (585/720 nt) yggN ← putative EcfF
RA 3,163,684 A→G intergenic (‑203/+31) plsC ← / ← parC 1‑acylglycerol‑3‑phosphate O‑acyltransferase/DNA topoisomerase IV subunit A
RA 3,187,989 A→T pseudogene (558/2434 nt) yqiG → putative outer membrane usher protein YqiG
RA 3,233,352 G→A R563H (CGC→CAC)  fadH → 2,4‑dienoyl‑CoA reductase
RA 3,246,806 C→T A52V (GCC→GTC)  exuR → DNA‑binding transcriptional repressor ExuR
RA 3,261,403 G→A A339V (GCG→GTG)  tdcE ← 2‑ketobutyrate formate‑lyase/pyruvate formate‑lyase 4
RA 3,270,488 (C)7→8 noncoding (105/377 nt) rnpB ← RNase P catalytic RNA component
RA 3,280,942 G→A pseudogene (242/402 nt) agaW → N‑acetyl‑D‑galactosamine specific PTS truncated enzyme IIC component
RA 3,354,487 C→T intergenic (‑437/‑238) yhcC ← / → gltB radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB
RA 3,388,726 A→G V134A (GTT→GCT)  aaeA ← aromatic carboxylic acid efflux pump membrane fusion protein
RA 3,389,335 C→T M1M (ATG→ATA) † aaeX ← DUF1656 domain‑containing protein AaeX
RA 3,443,320 C→T A260T (GCA→ACA)  secY ← Sec translocon subunit SecY
RA 3,541,362 T→C V319A (GTG→GCG)  feoB → Fe(2(+)) transporter FeoB
RA 3,557,086 A→G F332L (TTC→CTC)  rtcB ← RNA‑splicing ligase
RA 3,560,455 +G pseudogene (151/758 nt) glpR ← DNA‑binding transcriptional repressor GlpR
RA 3,616,067 T→C V276A (GTG→GCG)  nikB → Ni(2(+)) ABC transporter membrane subunit NikB
RA 3,754,800 T→C intergenic (‑372/+173) yiaW ← / ← aldB DUF3302 domain‑containing protein YiaW/aldehyde dehydrogenase B
RA 3,815,883 +C coding (667/687 nt) rph ← truncated RNase PH
RA 3,860,630 (C)5→4 coding (348/894 nt) yidL → putative DNA‑binding transcriptional regulator YidL
RA 3,893,082 G→A P106P (CCG→CCA)  yidZ → putative LysR‑type transcriptional regulator YidZ
RA 3,957,223 G→A P200S (CCG→TCG)  ilvY ← DNA‑binding transcriptional dual regulator IlvY
RA 4,048,215 T→C V417A (GTC→GCC)  polA → DNA polymerase I
RA 4,114,992 A→G C196C (TGT→TGC)  glpX ← fructose‑1,6‑bisphosphatase 2
RA 4,117,855 G→A A79V (GCC→GTC)  glpF ← glycerol facilitator
RA 4,219,155 A→G D187G (GAC→GGC)  aceK → isocitrate dehydrogenase kinase/phosphatase
RA 4,271,009 C→T L118F (CTC→TTC)  yjbR → PF04237 family protein YjbR
RA 4,278,113 A→G intergenic (‑47/‑366) ryjA ← / → ghxP small RNA RyjA/guanine/hypoxanthine transporter GhxP
RA 4,296,381 +GC intergenic (+587/+55) gltP → / ← yjcO glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
RA 4,298,452 G→A G305G (GGC→GGT)  fdhF ← formate dehydrogenase H
RA 4,322,037 A→G V129A (GTC→GCC)  phnF ← putative transcriptional regulator PhnF
RA 4,424,463 (C)5→4 intergenic (+77/+53) ulaF → / ← yjfY L‑ribulose‑5‑phosphate 4‑epimerase UlaF/DUF1471 domain‑containing protein YjfY
RA 4,445,549 A→G T480A (ACC→GCC)  tamB → translocation and assembly module subunit TamB
RA 4,465,243 T→C Y313C (TAC→TGC)  treB ← trehalose‑specific PTS enzyme IIBC component

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 226730–226968 228565–226988 21–1836 19 [18] [18] 19 rrlH 23S ribosomal RNA
* * ÷ NC_000913 2066538–2066706 2067184–2066726 21–647 19 [18] [18] 21 insH‑6 CP4‑44 prophage; IS5 transposase and trans‑activator
* * ÷ NC_000913 3423770–3424234 3424525–3424239 6–756 23 [18] [12] 24 [rrfD]–[rrlD] [rrfD],[rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =92 (1.100)26 (0.350) 20/244 1.9 26.2% coding (290/630 nt) ycfK e14 prophage; protein StfP
?NC_000913 1209619 = 65 (0.880)pseudogene (37/537 nt) stfE e14 prophage; putative side tail fiber protein fragment
* ? NC_000913 3363001 =123 (1.470)138 (1.670) 58/274 0.2 68.6% coding (195/2382 nt) yhcD putative fimbrial usher protein YhcD
?NC_000913 3766087 = 4 (0.050)coding (3905/4134 nt) rhsA rhs element protein RhsA
* ? NC_000913 = 3653230NA (NA)83 (0.990) 51/276 0.3 96.5% noncoding (1/1195 nt) IS5 repeat region
?NC_000913 = 3766089 3 (0.040)coding (3907/4134 nt) rhsA rhs element protein RhsA