breseq  version 0.24  revision cd15a9d216e1
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation freq annotation gene description
JC JC 16,972 IS150 (–) +3 bp 86.1% intergenic (‑14/‑514) mokC ← / → nhaA regulatory protein for HokC, overlaps CDS of hokC/pH‑dependent sodium/proton antiporter
RA 380,188 A→C 92.6% F239L (TTT→TTG araJ ← predicted transporter
RA 475,288 +G 100% coding (18/1677 nt) ybaL ← predicted transporter with NAD(P)‑binding Rossmann‑fold domain
MC JC 547,700 Δ8,224 bp 100% IS1‑mediated [nmpC][ECB_00513] [nmpC], ybcR, ybcS, ybcT, ybcU, ECB_00510, nohB, ECB_00512, [ECB_00513]
RA 649,391 T→A 100% I471F (ATC→TTC)  mrdA ← transpeptidase involved in peptidoglycan synthesis (penicillin‑binding protein 2)
RA 683,496 A→C 100% V65G (GTT→GGT)  nagC ← DNA‑binding transcriptional dual regulator, repressor of N‑acetylglucosamine
RA 851,606 G→A 18.4% S3F (TCT→TTT)  ybiU ← hypothetical protein
RA 1,248,380 A→C 87.0% D295E (GAT→GAG dhaM ← fused predicted dihydroxyacetone‑specific PTS enzymes: HPr component/EI component
RA 1,329,516 C→T 100% H33Y (CAC→TAC)  topA → DNA topoisomerase I
RA 1,370,728 G→T 17.0% W151L (TGG→TTG)  ycjN → predicted sugar transporter subunit: periplasmic‑binding component of ABC superfamily
JC JC 1,733,647 IS150 (–) +3 bp 100% coding (683‑685/1413 nt) pykF → pyruvate kinase
JC JC 1,821,525 IS150 (–) +3 bp 96.3% coding (573‑575/1041 nt) ynjI ← predicted inner membrane protein
RA 2,082,685 G→A 92.5% A494V (GCT→GTT)  yegI ← hypothetical protein
RA 3,155,168 G→A 93.0% G296S (GGC→AGC)  ebgR → DNA‑binding transcriptional repressor
JC 3,289,962 Δ16 bp 91.9% coding (96‑111/4554 nt) gltB → glutamate synthase, large subunit
RA 3,370,027 T→A 100% K117M (AAG→ATG)  rpsM ← 30S ribosomal protein S13
RA 3,483,047 C→A 100% R455S (CGC→AGC)  malT → transcriptional regulator MalT
RA 3,762,741 A→T 100% K662I (AAA→ATA)  spoT → bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
MC JC 3,894,997 Δ6,934 bp 100% IS150‑mediated rbsD[yieO] rbsD, rbsA, rbsC, rbsB, rbsK, rbsR, [yieO]
RA 3,901,931 G→T 6.8% T163T (ACC→ACA yieO ← predicted multidrug or homocysteine efflux system
RA 4,100,655 C→T 100% M192I (ATG→ATA hslU ← ATP‑dependent protease ATP‑binding subunit
RA 4,126,699 Δ1 bp 90.2% coding (335/879 nt) pflC → pyruvate formate lyase II activase
RA 4,141,009 G→A 23.6% E28K (GAA→AAA)  yijC → DNA‑binding transcriptional repressor
RA 4,201,911 C→T 81.5% A217T (GCG→ACG)  iclR ← DNA‑binding transcriptional repressor
JC JC 4,524,522 IS186 (+) +6 bp 93.5% coding (494‑499/549 nt) fimA → major type 1 subunit fimbrin (pilin)
RA 4,561,446 C→G 9.6% L1097L (CTG→CTC hsdR ← endonuclease R
RA 4,561,448 G→T 7.6% L1097M (CTG→ATG)  hsdR ← endonuclease R
RA 4,616,396 G→A 100% G290S (GGC→AGC)  nadR → nicotinamide‑nucleotide adenylyltransferase

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ REL606 240050 240202 153 22 [21] [20] 22 aspV/yafT tRNA‑Asp/predicted aminopeptidase
* * ÷ REL606 2031670–2031702 2035060–2034324 2623–3391 25 [21] [20] 23 [manB]–insA‑14 [manB], manC, insB‑14, insA‑14
* * ÷ REL606 2035094–2035096 2054970–2054943 19848–19877 90 [6] [21] 23 [wbbD]–[cpsG] 19 genes
[wbbD], wbbC, wzy, wbbB, wbbA, vioB, vioA, wzx, rmlC, rfbA, rfbD, rfbB, galF, wcaM, wcaL, wcaK, wzxC, wcaJ, [cpsG]
* * ÷ REL606 3022431 3023224 794 22 [20] [21] 22 [ECB_02821] [ECB_02821]

Unassigned new junction evidence...
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? REL606 = 16728NA (NA)37 (0.700) 27/60 NT 49.3% noncoding (1343/1343 nt) IS186 repeat region
?REL606 2713428 = 38 (0.610)noncoding (77/93 nt) serV tRNA‑Ser
* ? REL606 = 237270 (0.000)31 (0.550) 22/64 NT 100% noncoding (437/768 nt) IS1 repeat region
?REL606 = 666130 NA (NA)noncoding (1443/1443 nt) IS150 repeat region
* ? REL606 = 12231153 (0.880)5 (0.080) 3/68 NT 11.1% coding (227/855 nt) ampE predicted inner membrane protein
?REL606 4291982 = 27 (0.440)intergenic (‑169/‑190) rpiR/rpiB DNA‑binding transcriptional repressor/ribose‑5‑phosphate isomerase B
* ? REL606 221948 =52 (0.870)4 (0.070) 4/68 NT 7.9% coding (487/708 nt) yaeB hypothetical protein
?REL606 4351442 = 41 (0.660)intergenic (+50/‑88) groEL/yjeI chaperonin GroEL/hypothetical protein
* ? REL606 241691 =0 (0.000)60 (1.030) 36/66 NT 100% noncoding (435/768 nt) IS1 repeat region
?REL606 3893554 = NA (NA)noncoding (1/1443 nt) IS150 repeat region
* ? REL606 308482 =54 (0.870)7 (0.110) 3/70 NT 14.1% coding (554/606 nt) yahD predicted transcriptional regulator with ankyrin domain
?REL606 1580990 = 31 (0.500)coding (757/1389 nt) yneI predicted aldehyde dehydrogenase
* ? REL606 370838 =32 (0.570)4 (0.070) 3/64 NT 10.8% intergenic (+30/‑89) phoA/psiF bacterial alkaline phosphatase/hypothetical protein
?REL606 3051517 = 34 (0.550)coding (835/1224 nt) glcF glycolate oxidase iron‑sulfur subunit
* ? REL606 417727 =39 (0.820)6 (0.130) 5/54 NT 15.2% coding (682/891 nt) cyoE protoheme IX farnesyltransferase
?REL606 1333598 = 28 (0.450)pseudogene (67/129 nt) yciX predicted protein; b4522(b4574)
* ? REL606 546191 =54 (0.960)3 (0.050) 3/64 NT 5.3% coding (346/384 nt) ybcQ predicted antitermination protein
?REL606 4521571 = NA (NA)noncoding (768/768 nt) IS1 repeat region
* ? REL606 556412 =42 (0.790)7 (0.130) 5/60 NT 15.7% coding (1697/2346 nt) ECB_00513 conserved hypothetical protein
?REL606 1539626 = 33 (0.530)coding (46/2400 nt) dos cAMP phosphodiesterase, heme‑regulated
* ? REL606 619117 =NA (NA)9 (0.150) 8/66 NT 15.8% noncoding (768/768 nt) IS1 repeat region
?REL606 = 2997448 48 (0.780)coding (116/903 nt) ECB_02798 conserved hypothetical protein
* ? REL606 640118 =43 (0.790)9 (0.160) 6/62 NT 23.1% intergenic (+36/+19) cspE/ccrB cold shock protein E/camphor resistance protein CrcB
?REL606 = 1245375 17 (0.280)coding (66/441 nt) ycgY hypothetical protein
* ? REL606 = 70145436 (0.600)9 (0.150) 5/68 NT 32.7% coding (1102/2199 nt) speF ornithine decarboxylase isozyme, inducible
?REL606 2039202 = 1 (0.020)coding (493/747 nt) wbbA putative glycosyltransferase WbbA
* ? REL606 = 78351035 (0.710)6 (0.120) 4/56 NT 12.8% coding (995/1434 nt) ybhI predicted transporter
?REL606 = 4141016 47 (0.760)coding (89/705 nt) yijC DNA‑binding transcriptional repressor
* ? REL606 = 78449026 (0.460)3 (0.050) 3/64 NT 9.0% coding (359/2262 nt) ybhJ predicted hydratase
?REL606 3912266 = 35 (0.570)intergenic (+46/‑94) ilvL/ilvG ilvG operon leader peptide/acetolactate synthase II, valine insensitive, large subunit
* ? REL606 = 84006434 (0.600)6 (0.110) 5/64 NT 14.0% coding (566/747 nt) glnH glutamine ABC transporter periplasmic protein
?REL606 2842326 = 40 (0.650)intergenic (+24/+50) metV/amiC tRNA‑Met/N‑acetylmuramoyl‑L‑alanine amidase
* ? REL606 885072 =27 (0.510)9 (0.170) 5/60 NT 25.7% coding (35/858 nt) ECB_00824 protein similar to retron EC67 DNA adenine methylase
?REL606 3944634 = 25 (0.400)intergenic (+23/‑124) proM/aslB tRNA‑Pro/predicted regulator of arylsulfatase activity
* ? REL606 = 103607332 (0.580)13 (0.240) 8/62 NT 29.2% intergenic (+45/+31) ycbG/ompA hypothetical protein/outer membrane protein A (3a;II*;G;d)
?REL606 = 2540943 31 (0.500)coding (38/1290 nt) uraA uracil transporter
* ? REL606 1097109 =34 (0.740)5 (0.110) 4/52 NT 12.0% intergenic (+12/‑522) putP/ycdN proline:sodium symporter/putative membrane protein
?REL606 4079105 = 39 (0.630)coding (903/1035 nt) rhaT L‑rhamnose:proton symporter
* ? REL606 1241877 =37 (0.750)8 (0.160) 3/56 NT 19.5% coding (345/1737 nt) ycgO potassium/proton antiporter
?REL606 = 4081036 29 (0.470)intergenic (+124/‑136) sodA/kdgT superoxide dismutase, Mn/2‑keto‑3‑deoxygluconate permease
* ? REL606 1286705 =46 (0.930)8 (0.160) 6/56 NT 20.0% intergenic (+29/‑154) narI/ECB_01206 nitrate reductase 1, gamma (cytochrome b(NR)) subunit/hypothetical protein
?REL606 1802338 = 18 (0.290)intergenic (‑136/+67) ydjR/spy hypothetical protein/envelope stress induced periplasmic protein
* ? REL606 1299694 =34 (0.740)11 (0.240) 5/52 NT 29.3% coding (919/1632 nt) oppA oligopeptide transporter subunit
?REL606 = 2574502 19 (0.310)intergenic (+344/+474) sseA/sseB 3‑mercaptopyruvate sulfurtransferase/rhodanase‑like enzyme, sulfur transfer from thiosulfate
* ? REL606 1474796 =37 (0.750)6 (0.120) 4/56 NT 17.1% coding (1030/1209 nt) ydcM predicted transposase
?REL606 = 2574503 21 (0.340)intergenic (+345/+473) sseA/sseB 3‑mercaptopyruvate sulfurtransferase/rhodanase‑like enzyme, sulfur transfer from thiosulfate
* ? REL606 1525665 =73 (1.250)11 (0.190) 11/66 NT 13.8% coding (178/654 nt) fdnI formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible
?REL606 = 1536792 65 (1.050)coding (223/582 nt) ddpX D‑ala‑D‑ala dipeptidase, Zn‑dependent
* ? REL606 1529587 =69 (1.120)5 (0.080) 4/70 NT 9.5% coding (21/1698 nt) sfcA malate dehydrogenase, (decarboxylating, NAD‑requiring) (malic enzyme)
?REL606 = 3061121 26 (0.420)coding (756/1173 nt) ECB_02854 conserved hypothetical protein
* ? REL606 = 161952944 (0.830)7 (0.130) 4/60 NT 15.6% intergenic (‑138/+79) rem/hokD predicted protein/small toxic polypeptide
?REL606 = 3069838 32 (0.520)coding (621/1500 nt) pitB phosphate transporter
* ? REL606 1955860 =31 (0.610)7 (0.140) 3/58 NT 15.2% coding (50/888 nt) motA flagellar motor protein MotA
?REL606 = 4141016 47 (0.760)coding (89/705 nt) yijC DNA‑binding transcriptional repressor
* ? REL606 1980072 =40 (0.780)10 (0.200) 7/58 NT 18.5% intergenic (+48/‑295) yodA/yodB conserved metal‑binding protein/predicted cytochrome
?REL606 4038529 = 48 (0.780)intergenic (+41/‑176) bipA/yihL GTP‑binding protein/predicted DNA‑binding transcriptional regulator
* ? REL606 2039192 =1 (0.020)11 (0.190) 8/64 NT 53.7% coding (503/747 nt) wbbA putative glycosyltransferase WbbA
?REL606 2353393 = 18 (0.290)coding (1551/1833 nt) yfbS predicted transporter
* ? REL606 = 277140956 (1.060)4 (0.080) 3/60 NT 8.2% intergenic (‑219/‑33) cysD/iap sulfate adenylyltransferase subunit 2/aminopeptidase in alkaline phosphatase isozyme conversion
?REL606 4412609 = 34 (0.550)intergenic (‑376/‑158) ECB_04076/ytfA putative oxoacyl reductase/predicted transcriptional regulator
* ? REL606 2822187 =NA (NA)32 (0.570) 26/64 NT 54.2% noncoding (768/768 nt) IS1 repeat region
?REL606 = 2997504 27 (0.440)coding (172/903 nt) ECB_02798 conserved hypothetical protein
* ? REL606 = 287442124 (0.450)9 (0.170) 4/60 NT 21.7% coding (780/936 nt) lysR DNA‑binding transcriptional dual regulator
?REL606 3419921 = 41 (0.660)coding (282/573 nt) ppiA peptidyl‑prolyl cis‑trans isomerase A (rotamase A)
* ? REL606 = 288616747 (0.950)6 (0.120) 4/56 NT 13.3% coding (68/2259 nt) xdhA xanthine dehydrogenase, molybdenum binding subunit
?REL606 3650766 = 31 (0.500)intergenic (+47/+140) cspA/hokA major cold shock protein/toxic polypeptide, small
* ? REL606 3082514 =43 (0.810)8 (0.150) 5/60 NT 15.1% coding (446/1041 nt) yghZ aldo‑keto reductase
?REL606 = 4141016 47 (0.760)coding (89/705 nt) yijC DNA‑binding transcriptional repressor
* ? REL606 3198500 =48 (0.880)10 (0.180) 5/62 NT 23.8% coding (563/990 nt) tdcB threonine dehydratase
?REL606 3424874 = 16 (0.260)intergenic (+92/‑34) nirD/nirC nitrite reductase small subunit/nitrite transporter
* ? REL606 3367495 =31 (0.590)4 (0.080) 4/60 NT 10.8% intergenic (‑81/+26) yhdN/rplQ hypothetical protein/50S ribosomal protein L17
?REL606 3725714 = 35 (0.570)coding (68/432 nt) yibN predicted rhodanese‑related sulfurtransferase
* ? REL606 3893549 =NA (NA)3 (0.060) 3/60 NT NA intergenic (+4/‑52) kup/insJ‑5 potassium transporter/IS150 hypothetical protein
?REL606 = 3894994 NA (NA)noncoding (1441/1443 nt) IS150 repeat region
* ? REL606 3995530 =46 (0.870)10 (0.190) 4/60 NT 17.7% coding (58/768 nt) ECB_03724 putative transcriptional regulator
?REL606 = 4141016 47 (0.760)coding (89/705 nt) yijC DNA‑binding transcriptional repressor