breseq  version 0.35.7  revision b7a44cd89118
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation annotation gene description
RA 2,450 G→T L705L (CTG→CTT thrA → bifunctional aspartokinase I/homeserine dehydrogenase I
RA 45,662 C→T V155I (GTC→ATC)  caiT ← L‑carnitine/gamma‑butyrobetaine antiporter
RA 70,867 T→C D92G (GAC→GGC)  araA ← L‑arabinose isomerase
JC JC 183,262 IS150 (+) +3 bp coding (1184‑1186/1518 nt) dgt → deoxyguanosinetriphosphate triphosphohydrolase
RA 226,159 C→A P163T (CCT→ACT)  gmhB → hypothetical protein
RA 239,002 A→C A4A (GCA→GCC dnaQ → DNA polymerase III subunit epsilon
JC JC 336,055 IS150 (–) +3 bp coding (2805‑2807/3075 nt) lacZ ← beta‑D‑galactosidase
RA 393,720 G→A R96H (CGC→CAC)  queA → S‑adenosylmethionine:tRNA ribosyltransferase‑isomerase
RA 430,835 C→T intergenic (‑48/‑108) insL‑2 ← / → lon putative transposase insL for insertion sequence IS186/DNA‑binding ATP‑dependent protease La
RA 433,668 C→T R55C (CGT→TGT)  hupB → HU, DNA‑binding transcriptional regulator, beta subunit
MC JC JC 490,484 IS150 (+) Δ1 bp :: +CATT intergenic (‑37/+24) ybbN ← / ← ybbO predicted thioredoxin domain‑containing protein/short chain dehydrogenase
JC JC 502,543 IS150 (–) +3 bp coding (848‑850/1095 nt) ybbB ← tRNA 2‑selenouridine synthase, selenophosphate‑dependent
MC JC 547,700 Δ8,125 bp IS1‑mediated [nmpC][ECB_00513] [nmpC], ybcR, ybcS, ybcT, ybcU, ECB_00510, nohB, ECB_00512, [ECB_00513]
RA 588,492 +AA intergenic (‑219/‑50) ybdK ← / → insJ‑1 gamma‑glutamyl:cysteine ligase/IS150 hypothetical protein
JC JC 651,703 +GAA :: IS150 (+) +2 bp intergenic (‑83/+176) ybeB ← / ← phpB hypothetical protein/predicted alpha‑ribazole‑5'‑P phosphatase
RA 666,133 +T pseudogene (355/387 nt) gltL ← ATP‑binding protein of glutamate/aspartate transport system; b0652_1
RA 735,660 T→A intergenic (‑401/‑308) gltA ← / → sdhC citrate synthase/succinate dehydrogenase cytochrome b556 large membrane subunit
RA 761,693 T→G noncoding (47/76 nt) valT → tRNA‑Val
RA 796,336 (T)8→7 intergenic (‑7/‑419) ECB_00737 ← / → ECB_00738 hypothetical protein/hypothetical protein
RA 875,094 G→C H65D (CAT→GAT)  deoR ← DNA‑binding transcriptional repressor
JC JC 896,463 IS150 (+) +3 bp coding (159‑161/432 nt) ECB_00838 → putative phage tail protein
JC JC 929,574 IS150 (+) +3 bp coding (946‑948/1653 nt) hcp ← hydroxylamine reductase
RA 943,554 A→C intergenic (‑53/+232) infA ← / ← aat translation initiation factor IF‑1/leucyl/phenylalanyl‑tRNA‑protein transferase
RA 950,280 T→G intergenic (+133/‑2) lrp → / → ftsK DNA‑binding transcriptional dual regulator, leucine‑binding/DNA‑binding membrane protein required for chromosome resolution and partitioning
RA 962,002 G→A intergenic (+13/+22) dmsC → / ← ycaC dimethyl sulfoxide reductase, anaerobic, subunit C/predicted hydrolase
JC JC 969,836 IS150 (+) +3 bp coding (810‑812/2283 nt) pflB ← pyruvate formate lyase I
JC JC 1,102,032 IS150 (–) +3 bp coding (756‑758/1065 nt) phoH → conserved protein with nucleoside triphosphate hydrolase domain
RA 1,166,129 T→C intergenic (+156/‑55) fabG → / → acpP 3‑oxoacyl‑[acyl‑carrier‑protein] reductase/acyl carrier protein
RA 1,207,861 T→G N47T (AAC→ACC)  ycfC ← hypothetical protein
JC JC 1,218,697 IS150 (+) +3 bp coding (1209‑1211/1524 nt) ycgG → conserved inner membrane protein
RA 1,343,489 G→A L542L (CTG→TTG)  yciR ← modulator of Rnase II stability
JC JC 1,354,425 IS150 (–) +3 bp coding (1053‑1055/1644 nt) sapA ← predicted antimicrobial peptide transporter subunit
JC JC 1,462,266 IS150 (+) +3 bp intergenic (‑28/‑311) mokB ← / → trg regulatory peptide/methyl‑accepting chemotaxis protein III, ribose and galactose sensor receptor
MC 1,609,175 Δ7,554 bp between IS3 ybcW[ECB_01526] ybcW, gnsB, ynfN, ECB_01516, cspI, ydfP, ydfQ, ydfR, essQ, ECB_01522, ECB_01523, insE‑4, insF‑4, [ECB_01526]
JC JC 1,619,834 IS150 (–) +3 bp intergenic (‑71/+139) hokD ← / ← ECB_01533 small toxic polypeptide/conserved hypothetical protein
RA 1,733,865 G→T A301S (GCC→TCC)  pykF → pyruvate kinase
RA 1,746,189 G→A intergenic (‑237/‑152) ydiJ ← / → ydiK predicted FAD‑linked oxidoreductase/predicted inner membrane protein
RA 1,749,019 G→A pseudogene (326/858 nt) ydiM → putative transport protein (MFS family); b1690_1
RA 1,879,026 T→A D380V (GAT→GTT)  yoaE ← fused predicted membrane protein/conserved protein
RA 1,902,276 (T)7→8 coding (7/342 nt) yebY ← hypothetical protein
RA 1,915,108 (A)8→7 intergenic (‑218/‑120) zwf ← / → yebK glucose‑6‑phosphate 1‑dehydrogenase/predicted DNA‑binding transcriptional regulator
RA 1,916,109 A→G intergenic (+12/‑116) yebK → / → pykA predicted DNA‑binding transcriptional regulator/pyruvate kinase
RA 1,930,575 C→A F137L (TTC→TTA yecE → hypothetical protein
RA 1,948,728 T→C M343V (ATG→GTG)  tap ← methyl‑accepting protein IV
MC JC 1,974,040 Δ8,273 bp IS1‑mediated [yedU][yeeI] [yedU], yedV, yedW, yedX, yedY, yedZ, yodA, yodB, serU, [yeeI]
MC JC 2,034,358 Δ19,491 bp [insB‑14][wcaJ] 20 genes
JC JC 2,196,656 IS150 (–) +3 bp coding (1350‑1352/1992 nt) cirA ← ferric iron‑catecholate outer membrane transporter
RA 2,268,951 T→G I129S (ATC→AGC)  atoC → fused response regulator of ato operon, in two‑component system with AtoS: response regulator/sigma54 interaction protein
MC JC JC 2,397,529 IS150 (–) Δ14 bp coding (1124‑1137/2646 nt) yfcTU ← predicted outer membrane export usher protein
JC JC 2,405,131 IS1 (–) +9 bp coding (168‑176/1347 nt) fadL → long‑chain fatty acid outer membrane transporter
JC JC 2,448,493 IS186 (–) +6 bp intergenic (+24/+21) nupC → / ← yfeA nucleoside (except guanosine) transporter/predicted diguanylate cyclase
JC JC 2,522,900 IS150 (–) +3 bp coding (255‑257/2019 nt) hyfB → NADH dehydrogenase subunit N
RA 2,702,361 G→A G160S (GGC→AGC)  proX → glycine betaine transporter subunit
RA 2,758,314 A→C K374Q (AAA→CAA)  ygbK → hypothetical protein
RA 2,775,879 Δ1 bp intergenic (‑49/+200) insJ‑3 ← / ← cysH IS150 hypothetical protein/phosphoadenosine phosphosulfate reductase
RA 2,847,052 A→G V10A (GTT→GCT)  recD ← exonuclease V (RecBCD complex), alpha chain
RA 3,067,926 G→A A40V (GCA→GTA)  yghS ← predicted protein with nucleoside triphosphate hydrolase domain
RA 3,093,020 T→G F74L (TTT→TTG yqhH → predicted outer membrane lipoprotein
RA 3,095,121 G→T C66* (TGC→TGA ygiQ ← hypothetical protein
RA 3,176,730 T→C Y349C (TAC→TGC)  uxaC ← glucuronate isomerase
JC JC 3,270,443 IS150 (–) +4 bp intergenic (+21/+24) nlp → / ← murA DNA‑binding transcriptional activator of maltose metabolism/UDP‑N‑acetylglucosamine 1‑carboxyvinyltransferase
RA 3,271,926 T→C D38G (GAC→GGC)  yrbA ← predicted DNA‑binding transcriptional regulator
RA 3,287,483 T→C M260V (ATG→GTG)  arcB ← hybrid sensory histidine kinase in two‑component regulatory system with ArcA
RA 3,308,106 G→A A6A (GCG→GCA yhcB → hypothetical protein
RA 3,312,775 G→A R59H (CGC→CAC)  argR → arginine repressor
RA 3,328,272 A→G V236A (GTT→GCT)  mreB ← cell wall structural complex MreBCD, actin‑like component MreB
RA 3,338,108 T→G intergenic (+266/‑63) prmA → / → yhdG ribosomal protein L11 methyltransferase/tRNA‑dihydrouridine synthase B
RA 3,407,065 T→C E483G (GAA→GGA)  kefB ← glutathione‑regulated potassium‑efflux system protein
RA 3,409,316 T→G S41S (TCT→TCG yheS → fused predicted transporter subunits of ABC superfamily: ATP‑binding components
MC JC 3,482,398 Δ25 bp coding (714‑738/2706 nt) malT → transcriptional regulator MalT
RA 3,536,881 A→G E148G (GAA→GGA)  yhhN → conserved inner membrane protein
JC JC 3,537,178 +GTACTGACCCCAAAA :: IS150 (–) :: +CAA coding (40/2199 nt) zntA → zinc, cobalt and lead efflux system
RA 3,684,366 C→A R216S (CGT→AGT)  ECB_03438 → conserved hypothetical protein
RA 3,724,534 C→T G121S (GGT→AGT)  secB ← export protein SecB
JC JC 3,766,595 IS150 (+) +3 bp coding (1111‑1113/1206 nt) gltS ← glutamate transporter
JC JC 3,841,192 IS150 (+) +3 bp coding (389‑391/1074 nt) recF ← recombination protein F
MC JC 3,894,997 Δ6,138 bp IS150‑mediated rbsD[yieO] rbsD, rbsA, rbsC, rbsB, rbsK, rbsR, [yieO]
JC 3,947,872 (TAATTGA)2→3 intergenic (‑66/+620) aslA ← / ← hemY acrylsulfatase‑like enzyme/predicted protoheme IX synthesis protein
JC JC 3,981,782 IS150 (–) +3 bp coding (249‑251/1224 nt) ECB_03710 ← putative permease
JC JC 3,990,387 IS150 (+) +3 bp coding (1250‑1252/1491 nt) ECB_03719 ← conserved hypothetical protein
JC JC 4,092,861 IS150 (+) +3 bp coding (87‑89/429 nt) yiiT → stress‑induced protein
RA 4,096,877 G→T Y232* (TAC→TAA glpF ← glycerol facilitator
RA 4,101,091 T→C E47G (GAA→GGA)  hslU ← ATP‑dependent protease ATP‑binding subunit
RA 4,133,104 G→A R34R (CGC→CGT ppc ← phosphoenolpyruvate carboxylase
RA 4,201,980 G→A P194S (CCT→TCT)  iclR ← DNA‑binding transcriptional repressor
MC JC 4,205,069 Δ5 bp coding (2311‑2315/3684 nt) metH → B12‑dependent methionine synthase
MC JC 4,275,717 57510 bp→5 bp [yjcO][lysU] 52 genes
RA 4,384,430 C→A S29Y (TCT→TAT)  yjeB → predicted DNA‑binding transcriptional regulator
JC JC 4,415,710 IS150 (–) +3 bp coding (848‑850/1413 nt) cycA → D‑alanine/D‑serine/glycine transporter
RA 4,459,658 A→G P315P (CCA→CCG yjgL → hypothetical protein
JC JC 4,462,655 IS1 (+) +9 bp intergenic (‑85/‑100) yjgM ← / → yjgN predicted acetyltransferase/conserved inner membrane protein
RA 4,558,781 (T)7→6 coding (657/1425 nt) hsdS ← specificity determinant for hsdM and hsdR
JC JC 4,615,673 IS150 (+) +4 bp coding (145‑148/1233 nt) nadR → nicotinamide‑nucleotide adenylyltransferase
RA 4,628,460 T→G T3P (ACC→CCC)  arcA ← DNA‑binding response regulator in two‑component regulatory system with ArcB or CpxA

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ REL606 16975 18001 1027 84 [0] [0] 74 [nhaA] [nhaA]
* * ÷ REL606 762185–762230 762441–762361 132–257 34 [30] [29] 33 [lysZ]–lysQ [lysZ],lysQ
* * ÷ REL606 2086866–2086932 2093026 6095–6161 34 [31] [0] 72 yegM–[yegO] yegM,yegN,[yegO]
* * ÷ REL606 2655705 2655780 76 73 [0] [0] 107 [yfiH] [yfiH]
* * ÷ REL606 2842025–2842086 2842276–2842224 139–252 34 [31] [32] 34 [metZ]–[metV] [metZ],metW,[metV]
* * ÷ REL606 2999597 3048488 48892 116 [1] [0] 79 [flu]–yghK [flu],yeeR,ECB_02802,yafZ,ECB_02804,yeeS,yeeT,yeeU,yeeV,yeeW,ECB_02810,ECB_02811,ECB_02812,ECB_02813,ECB_02814,ECB_02815,ECB_02816,ECB_02817,ECB_02818,ECB_02819,ECB_02820,ECB_02821,ECB_02822,insB‑22,insA‑22,ECB_02825,ECB_02826,ECB_02827,ECB_02828,yghD,yghE,ECB_02831,ECB_02832,ECB_02833,ECB_02834,ECB_02835,ECB_02836,ECB_02837,ECB_02838,yghF,yghG,pppA,yghJ,yghK
* * ÷ REL606 4047676 4049579 1904 117 [0] [0] 115 [yihR]–[yihS] [yihR],[yihS]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? REL606 = 169740 (0.000)80 (1.050) 56/96 0.1 100% intergenic (‑16/‑514) mokC/nhaA regulatory protein for HokC, overlaps CDS of hokC/pH‑dependent sodium/proton antiporter
?REL606 = 590471 NA (NA)noncoding (1977/1977 nt) IS150 repeat region
* ? REL606 18002 =0 (0.000)74 (0.930) 50/100 0.3 100% coding (515/1167 nt) nhaA pH‑dependent sodium/proton antiporter
?REL606 588495 = NA (NA)noncoding (1/1977 nt) IS150 repeat region
* ? REL606 588495 =NA (NA)161 (2.110) 75/96 0.0 NA noncoding (1/1977 nt) IS150 repeat region
?REL606 589936 = NA (NA)noncoding (387/768 nt) IS1 repeat region
* ? REL606 = 589939NA (NA)74 (0.950) 50/98 0.3 NA noncoding (384/768 nt) IS1 repeat region
?REL606 = 590471 NA (NA)noncoding (1977/1977 nt) IS150 repeat region
* ? REL606 664688 =NA (NA)69 (0.900) 48/96 0.3 100% noncoding (1/1443 nt) IS150 repeat region
?REL606 1270660 = 0 (0.000)intergenic (‑167/+238) ldrC/chaA toxic polypeptide, small/calcium/sodium:proton antiporter
* ? REL606 664688 =NA (NA)73 (0.920) 50/100 0.3 NA noncoding (1/1443 nt) IS150 repeat region
?REL606 = 2086597 NA (NA)intergenic (‑1018/‑527) yegL/yegM hypothetical protein/multidrug efflux system, subunit A
* ? REL606 2093027 =0 (0.000)71 (0.890) 49/100 0.4 100% coding (1534/3078 nt) yegO multidrug efflux system, subunit C
?REL606 2774435 = NA (NA)noncoding (1443/1443 nt) IS150 repeat region
* ? REL606 2103888 =45 (0.560)58 (0.740)
+G
43/98 0.6 57.4% coding (155/216 nt) ECB_01992 hypothetical protein
?REL606 = 2103918 43 (0.540)coding (185/216 nt) ECB_01992 hypothetical protein
* ? REL606 = 26557040 (0.000)65 (0.830) 42/98 0.7 100% intergenic (‑123/+7) clpB/yfiH protein disaggregation chaperone/hypothetical protein
?REL606 3651091 = NA (NA)noncoding (1/1443 nt) IS150 repeat region
* ? REL606 2655781 =0 (0.000)98 (1.280) 51/96 0.2 100% coding (662/732 nt) yfiH hypothetical protein
?REL606 2774435 = NA (NA)noncoding (1443/1443 nt) IS150 repeat region
* ? REL606 2774435 =NA (NA)67 (0.900) 49/94 0.2 NA noncoding (1443/1443 nt) IS150 repeat region
?REL606 = 2822512 NA (NA)noncoding (443/768 nt) IS1 repeat region
* ? REL606 2774435 =NA (NA)114 (1.430) 63/100 0.0 99.1% noncoding (1443/1443 nt) IS150 repeat region
?REL606 = 2999596 1 (0.010)coding (33/2847 nt) flu antigen 43 (Ag43) phase‑variable biofilm formation autotransporter
* ? REL606 = 2775877NA (NA)72 (0.900) 53/100 0.2 100% noncoding (1/1443 nt) IS150 repeat region
?REL606 3048489 = 0 (0.000)intergenic (‑318/+37) yghK/glcB glycolate transporter/malate synthase
* ? REL606 = 3630716NA (NA)65 (0.820) 50/100 0.3 NA intergenic (‑171/‑305) ldrD/yhjV toxic polypeptide, small/predicted transporter
?REL606 = 3652533 NA (NA)noncoding (1443/1443 nt) IS150 repeat region
* ? REL606 3651091 =NA (NA)119 (1.490) 59/100 0.1 NA noncoding (1/1443 nt) IS150 repeat region
?REL606 3697154 = NA (NA)coding (278/4134 nt) rhsA rhsA element core protein RshA
* ? REL606 3651091 =NA (NA)114 (1.430) 63/100 0.0 100% noncoding (1/1443 nt) IS150 repeat region
?REL606 = 4047675 0 (0.000)coding (874/927 nt) yihR predicted aldose‑1‑epimerase
* ? REL606 = 3652533NA (NA)199 (2.500) 78/100 0.0 NA noncoding (1443/1443 nt) IS150 repeat region
?REL606 = 3697156 NA (NA)coding (280/4134 nt) rhsA rhsA element core protein RshA
* ? REL606 3697156 =NA (NA)125 (1.570) 64/100 0.0 NA coding (280/4134 nt) rhsA rhsA element core protein RshA
?REL606 3893553 = NA (NA)intergenic (+8/‑48) kup/insJ‑5 potassium transporter/IS150 hypothetical protein
* ? REL606 = 3894996NA (NA)113 (1.420) 57/100 0.1 100% noncoding (1443/1443 nt) IS150 repeat region
?REL606 4049580 = 0 (0.000)coding (324/1242 nt) yihS predicted glucosamine isomerase
* ? REL606 4034655 =115 (1.440)112 (1.440) 65/98 0.0 53.6% intergenic (‑58/+228) glnL/glnA sensory histidine kinase in two‑component regulatory system with GlnG/glutamine synthetase
?REL606 = 4034991 81 (1.040)coding (1302/1410 nt) glnA glutamine synthetase