breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation freq annotation gene description
MC JC 257,908 Δ776 bp 100% [crl] [crl]
RA 680,882 G→A 28.6% R224H (CGC→CAC)  djlC → J domain‑containing HscC co‑chaperone; Hsc56
RA 1,071,555 G→A 36.4% H71Y (CAT→TAT)  rutD ← putative reactive intermediate detoxifying aminoacrylate hydrolase
MC JC 1,299,499 Δ1,199 bp 100% intergenic (+254/‑485) ychE → / → oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
RA 1,685,527 A→G 100% G354G (GGT→GGC)  fumC ← fumarate hydratase (fumarase C),aerobic Class II
RA 1,795,227 A→T 44.5% intergenic (‑75/+26) btuC ← / ← ihfA vitamin B12 ABC transporter permease/integration host factor (IHF), DNA‑binding protein, alpha subunit
RA 1,795,228 G→C 44.5% intergenic (‑76/+25) btuC ← / ← ihfA vitamin B12 ABC transporter permease/integration host factor (IHF), DNA‑binding protein, alpha subunit
RA 1,795,229 A→T 44.6% intergenic (‑77/+24) btuC ← / ← ihfA vitamin B12 ABC transporter permease/integration host factor (IHF), DNA‑binding protein, alpha subunit
MC JC 1,978,503 Δ776 bp 100% insB1–insA insB1, insA
RA 2,145,313 C→A 100% S683Y (TCC→TAC)  yegE → putative diguanylate cyclase
RA 2,173,361 Δ2 bp 100% pseudogene (1‑2/442 nt) gatC ← pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC
RA 2,318,095 C→G 100% L594F (TTG→TTC)  rcsC ← hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
RA 2,724,815 G→T 57.2% S311* (TCA→TAA)  kgtP ← alpha‑ketoglutarate transporter
RA 3,560,455:1 +G 100% intergenic (‑2/+1) glpR ← / ← glpR pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon
RA 3,736,322 G→T 10.9% intergenic (+165/+31) xylR → / ← bax xylose divergent operon transcriptional activator/putative glucosaminidase
RA 3,736,323 A→G 10.9% intergenic (+166/+30) xylR → / ← bax xylose divergent operon transcriptional activator/putative glucosaminidase
RA 3,736,324 C→T 10.9% intergenic (+167/+29) xylR → / ← bax xylose divergent operon transcriptional activator/putative glucosaminidase
RA 3,736,325 A→C 11.2% intergenic (+168/+28) xylR → / ← bax xylose divergent operon transcriptional activator/putative glucosaminidase
RA 3,774,207 C→T 8.4% intergenic (+13/‑217) mtlA → / → mtlD mannitol‑specific PTS enzyme: IIA, IIB and IIC components/mannitol‑1‑phosphate dehydrogenase, NAD‑dependent
RA 3,774,214 C→T 9.2% intergenic (+20/‑210) mtlA → / → mtlD mannitol‑specific PTS enzyme: IIA, IIB and IIC components/mannitol‑1‑phosphate dehydrogenase, NAD‑dependent
RA 3,774,215 A→G 9.3% intergenic (+21/‑209) mtlA → / → mtlD mannitol‑specific PTS enzyme: IIA, IIB and IIC components/mannitol‑1‑phosphate dehydrogenase, NAD‑dependent
RA 3,774,222 A→G 11.6% intergenic (+28/‑202) mtlA → / → mtlD mannitol‑specific PTS enzyme: IIA, IIB and IIC components/mannitol‑1‑phosphate dehydrogenase, NAD‑dependent
RA 3,776,162:1 +G 11.6% intergenic (+3/+9) mtlR → / ← yibT mannitol operon repressor/uncharacterized protein
RA 3,776,167 Δ1 bp 10.9% intergenic (+8/+4) mtlR → / ← yibT mannitol operon repressor/uncharacterized protein
RA 3,781,051 C→G 14.3% intergenic (+34/‑164) lldD → / → trmL L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent
RA 3,809,681 T→A 9.2% V381D (GTT→GAT) ‡ waaA → 3‑deoxy‑D‑manno‑octulosonic‑acid transferase (KDO transferase)
RA 3,809,682 T→A 7.4% V381V (GTT→GTA) ‡ waaA → 3‑deoxy‑D‑manno‑octulosonic‑acid transferase (KDO transferase)
RA 3,809,683 T→A 7.5% S382T (TCC→ACC)  waaA → 3‑deoxy‑D‑manno‑octulosonic‑acid transferase (KDO transferase)
RA 3,814,164 G→A 7.7% G78D (GGT→GAT)  dut → deoxyuridinetriphosphatase
RA 3,814,167 T→C 7.5% I79T (ATC→ACC)  dut → deoxyuridinetriphosphatase
RA 3,828,334 A→T 12.2% I111N (ATT→AAT)  gltS ← glutamate transporter
RA 3,832,188 A→T 8.2% intergenic (+22/+31) yicH → / ← yicI putative inner membrane‑anchored periplasmic AsmA family protein/putative alpha‑glucosidase
RA 4,296,380:1 +CG 100% intergenic (+586/+56) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,489,389 G→A 24.9% A225A (GCC→GCT)  yjgR ← DUF853 family protein with NTPase fold

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 46577 46590 14 2 [1] [0] 2 yaaU putative MFS sugar transporter; membrane protein
* * ÷ NC_000913 95189 95274 86 2 [1] [1] 2 murF UDP‑N‑acetylmuramoyl‑tripeptide:D‑alanyl‑D‑ alanine ligase
* * ÷ NC_000913 176243 176320 78 2 [1] [1] 2 clcA H(+)/Cl(‑) exchange transporter
* * ÷ NC_000913 248835 248875 41 2 [1] [1] 2 lfhA pseudogene, flagellar system protein, promoterless fragment; flagellar biosynthesis
* * ÷ NC_000913 370406 370439 34 2 [1] [1] 3 mhpB 2,3‑dihydroxyphenylpropionate 1,2‑dioxygenase
* * ÷ NC_000913 416053 416069 17 2 [1] [0] 2 sbcD exonuclease, dsDNA, ATP‑dependent
* * ÷ NC_000913 461666 461746 81 2 [0] [1] 2 [hupB] [hupB]
* * ÷ NC_000913 558119 558203 85 4 [1] [1] 2 folD/sfmA bifunctional 5,10‑methylene‑tetrahydrofolate dehydrogenase/ 5,10‑methylene‑tetrahydrofolate cyclohydrolase/FimA homolog, function unknown
* * ÷ NC_000913 866950 867056 107 3 [1] [1] 2 iaaA Isoaspartyl peptidase
* * ÷ NC_000913 893736 893776 41 2 [1] [1] 2 ybjN/potF negative regulator of motility; multicopy suppressor of coaA(Ts)/putrescine ABC transporter periplasmic binding protein
* * ÷ NC_000913 900728 900830 103 2 [1] [1] 2 artJ/artM arginine ABC transporter periplasmic binding protein/arginine ABC transporter permease
* * ÷ NC_000913 913871 913892 22 2 [1] [1] 4 hcp/ybjE hybrid‑cluster [4Fe‑2S‑2O] subunit of anaerobic terminal reductases/putative transporter
* * ÷ NC_000913 957675 957706 32 2 [0] [1] 2 serC 3‑phosphoserine/phosphohydroxythreonine aminotransferase
* * ÷ NC_000913 1055349 1055381 33 2 [1] [1] 2 torS hybrid sensory histidine kinase in two‑component regulatory system with TorR
* * ÷ NC_000913 1209582 1209618 37 2 [1] [0] 9 stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* * ÷ NC_000913 1238318 1238405 88 2 [1] [1] 2 dadA D‑amino acid dehydrogenase
* * ÷ NC_000913 1292675 1292703 29 2 [1] [1] 2 hns global DNA‑binding transcriptional dual regulator H‑NS
* * ÷ NC_000913 1312952 1313013 62 3 [0] [1] 2 yciC UPF0259 family inner membrane protein
* * ÷ NC_000913 1606231 1606309 79 2 [1] [0] 2 lsrF putative autoinducer‑2 (AI‑2) aldolase
* * ÷ NC_000913 1698103 1698208 106 2 [1] [0] 2 [malI] [malI]
* * ÷ NC_000913 1768266 1768271 6 2 [0] [1] 2 ydiJ putative FAD‑linked oxidoreductase
* * ÷ NC_000913 1965116 1965188 73 2 [1] [1] 2 flhB flagellin export apparatus, substrate specificity protein
* * ÷ NC_000913 2033903 2033945 43 2 [0] [1] 2 rseX/yedS sRNA antisense regulator of ompA and ompC translation, Hfq‑dependent/pseudogene, outer membrane protein homology; putative outer membrane protein
* * ÷ NC_000913 2083531 2083616 86 2 [1] [1] 3 sbcB exodeoxyribonuclease I; exonuclease I
* * ÷ NC_000913 2107855 2107861 7 2 [1] [1] 2 glf UDP‑galactopyranose mutase, FAD/NAD(P)‑binding
* * ÷ NC_000913 2137326 2137414 89 2 [1] [1] 2 wza/yegH colanic acid export protein; outer membrane auxillary lipoprotein/inner membrane protein
* * ÷ NC_000913 2176822 2176866 45 2 [1] [0] 2 gatY D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit
* * ÷ NC_000913 2229125 2229244 120 2 [1] [1] 2 yohP/dusC uncharacterized protein/tRNA‑dihydrouridine synthase C
* * ÷ NC_000913 2235971 2236007 37 2 [0] [1] 2 preA dihydropyrimidine dehydrogenase, NADH‑dependent, subunit C
* * ÷ NC_000913 2251294 2251382 89 3 [1] [0] 2 nfo endonuclease IV with intrinsic 3'‑5' exonuclease activity
* * ÷ NC_000913 2263984 2264048 65 2 [1] [0] 2 setB lactose/glucose efflux system
* * ÷ NC_000913 2306636 2306647 12 2 [1] [1] 2 mqo malate dehydrogenase, FAD/NAD(P)‑binding domain
* * ÷ NC_000913 2329412 2329418 7 2 [0] [1] 2 yfaQ tandem DUF2300 domain protein, putative host defense protein
* * ÷ NC_000913 2366643 2366665 23 2 [1] [1] 3 arnB uridine 5'‑(beta‑1‑threo‑pentapyranosyl‑4‑ulose diphosphate) aminotransferase, PLP‑dependent
* * ÷ NC_000913 2550717 2550787 71 2 [1] [1] 2 yfeY RpoE‑regulated lipoprotein
* * ÷ NC_000913 2625523 2625558 36 2 [0] [1] 3 ppx exopolyphosphatase
* * ÷ NC_000913 2774670 2774699 30 2 [1] [1] 3 yfjW CP4‑57 prophage; putative inner membrane protein
* * ÷ NC_000913 2780042 2780081 40 2 [1] [1] 2 ypjA adhesin‑like autotransporter
* * ÷ NC_000913 2896402 2896507 106 2 [1] [1] 2 ygcR putative flavoprotein
* * ÷ NC_000913 2904197 2904242 46 2 [1] [1] 2 ygcE/queE putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis
* * ÷ NC_000913 3184122 3184152 31 2 [0] [0] 2 ribB 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase
* * ÷ NC_000913 3423795–3424234 3424515–3424239 6–721 2 [1] [0] 2 [rrlD] [rrlD]
* * ÷ NC_000913 3558128 3558179 52 2 [0] [1] 2 rtcB/rtcR RNA‑splicing ligase/sigma 54‑dependent transcriptional regulator of rtcBA expression
* * ÷ NC_000913 4029477 4029514 38 2 [1] [1] 2 fadB fused 3‑hydroxybutyryl‑CoA epimerase/delta(3)‑cis‑delta(2)‑trans‑enoyl‑CoA isomerase/enoyl‑CoA hydratase/3‑hydroxyacyl‑CoA dehydrogenase
* * ÷ NC_000913 4488221 4488239 19 2 [1] [0] 2 lptG lipopolysaccharide export ABC permease
* * ÷ NC_000913 4638874 4638911 38 2 [1] [1] 2 creD inner membrane protein

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 591569 =20 (1.780)3 (0.280) 3/250 NT 13.9% coding (1610/2238 nt) nfrB bacteriophage N4 receptor, inner membrane subunit
?NC_000913 591595 = 18 (1.680)coding (1584/2238 nt) nfrB bacteriophage N4 receptor, inner membrane subunit
* ? NC_000913 = 7827399 (0.800)3 (0.270) 3/260 NT 25.1% coding (655/1044 nt) nadA quinolinate synthase, subunit A
?NC_000913 = 782765 9 (0.810)coding (681/1044 nt) nadA quinolinate synthase, subunit A
* ? NC_000913 = 92557310 (0.890)3 (0.290) 4/242 NT 23.8% intergenic (+33/+311) clpA/serW ATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity/tRNA‑Ser
?NC_000913 = 925585 10 (0.960)intergenic (+45/+299) clpA/serW ATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity/tRNA‑Ser
* ? NC_000913 1207790 =1 (0.090)9 (0.910) 9/230 NT 95.3% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 0 (0.000)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 3305904 =5 (0.440)3 (0.290) 3/244 NT 38.3% intergenic (‑87/+67) mtr/deaD tryptophan transporter of high affinity/ATP‑dependent RNA helicase
?NC_000913 3305929 = 5 (0.480)intergenic (‑112/+42) mtr/deaD tryptophan transporter of high affinity/ATP‑dependent RNA helicase
* ? NC_000913 3426836 =NA (NA)7 (0.660) 7/248 NT NA intergenic (‑53/+122) rrlD/alaU 23S ribosomal RNA of rrnD operon/tRNA‑Ala
?NC_000913 3426854 = NA (NA)intergenic (‑71/+104) rrlD/alaU 23S ribosomal RNA of rrnD operon/tRNA‑Ala
* ? NC_000913 3596422 =5 (0.440)3 (0.280) 3/248 NT 43.7% intergenic (‑19/+29) livH/livK branched‑chain amino acid ABC transporter permease/leucine transporter subunit
?NC_000913 3596443 = 3 (0.280)intergenic (‑40/+8) livH/livK branched‑chain amino acid ABC transporter permease/leucine transporter subunit
* ? NC_000913 3721045 =17 (1.510)51 (4.570) 46/260 NT 76.8% noncoding (413/1443 nt) IS150 repeat region
?NC_000913 = 3839774 14 (1.250)coding (220/819 nt) nlpA cytoplasmic membrane lipoprotein‑28
* ? NC_000913 = 3774359NA (NA)3 (0.280) 3/248 NT 5.3% intergenic (+165/‑65) mtlA/mtlD mannitol‑specific PTS enzyme: IIA, IIB and IIC components/mannitol‑1‑phosphate dehydrogenase, NAD‑dependent
?NC_000913 = 3774387 54 (5.070)intergenic (+193/‑37) mtlA/mtlD mannitol‑specific PTS enzyme: IIA, IIB and IIC components/mannitol‑1‑phosphate dehydrogenase, NAD‑dependent
* ? NC_000913 3813314 =33 (2.930)3 (0.270) 3/254 NT 9.0% coding (584/1221 nt) dfp fused 4'‑phosphopantothenoylcysteine decarboxylase/phosphopantothenoylcysteine synthetase, FMN‑binding
?NC_000913 3813344 = 29 (2.660)coding (614/1221 nt) dfp fused 4'‑phosphopantothenoylcysteine decarboxylase/phosphopantothenoylcysteine synthetase, FMN‑binding
* ? NC_000913 = 43664889 (0.800)3 (0.280) 3/250 NT 25.4% coding (286/1302 nt) dcuA C4‑dicarboxylate antiporter
?NC_000913 = 4366516 9 (0.840)coding (258/1302 nt) dcuA C4‑dicarboxylate antiporter