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
RA 204,556 A→G 100% intergenic (+156/‑28) alaV → / → rrlH tRNA‑Ala/23S ribosomal RNA
RA 1,763,556 T→C 61.5% noncoding (288/1542 nt) rrsG ← 16S ribosomal RNA
RA 1,892,019:1 +GC 100% intergenic (‑437/+54) gudP ← / ← ygdL predicted D‑glucarate transporter/conserved hypothetical protein
RA 2,359,867 G→A 42.9% noncoding (1228/2905 nt) rrlA ← 23S ribosomal RNA
RA 2,359,876 C→T 42.9% noncoding (1219/2905 nt) rrlA ← 23S ribosomal RNA

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ minE 5494 5559 66 2 [0] [1] 2 [yaaX] [yaaX]
* * ÷ minE 14269 14282 14 2 [1] [1] 2 dnaJ chaperone Hsp40, co‑chaperone with DnaK
* * ÷ minE 64483 64498 16 2 [1] [1] 2 leuC 3‑isopropylmalate isomerase subunit, dehydratase component
* * ÷ minE 78927 78952 26 2 [1] [1] 3 murE UDP‑N‑acetylmuramoyl‑L‑alanyl‑D‑glutamate:meso‑ diaminopimelate ligase
* * ÷ minE 145684 145713 30 2 [1] [1] 2 sfsA predicted DNA‑binding transcriptional regulator
* * ÷ minE 184582 184653 72 2 [1] [1] 2 dnaE DNA polymerase III alpha subunit
* * ÷ minE 193964 193986 23 2 [1] [1] 2 yaeJ conserved hypothetical protein
* * ÷ minE 221460 221489 30 2 [1] [1] 2 fadE acyl coenzyme A dehydrogenase
* * ÷ minE 252009 252034 26 2 [1] [1] 2 malZ maltodextrin glucosidase
* * ÷ minE 341130 341151 22 2 [1] [1] 2 ybaT predicted transporter
* * ÷ minE 349678 349701 24 2 [1] [0] 2 hyi hydroxypyruvate isomerase
* * ÷ minE 379496 379514 19 4 [1] [1] 2 fepB/entC iron‑enterobactin transporter subunit/isochorismate synthase 1
* * ÷ minE 410996 411012 17 2 [1] [1] 2 leuS leucyl‑tRNA synthetase
* * ÷ minE 444391 444416 26 2 [1] [0] 2 kdpE DNA‑binding response regulator in two‑component regulatory system with KdpD
* * ÷ minE 454551 454572 22 2 [1] [0] 2 ybgH predicted transporter
* * ÷ minE 465964 466005 42 2 [1] [1] 2 sucA 2‑oxoglutarate decarboxylase, thiamin‑requiring
* * ÷ minE 483625 483681 57 2 [1] [1] 3 tolA membrane anchored protein in TolA‑TolQ‑TolR complex
* * ÷ minE 519525 519577 53 2 [1] [1] 2 bioD/uvrB dethiobiotin synthetase/excinulease of nucleotide excision repair, DNA damage recognition component
* * ÷ minE 520854 520866 13 2 [1] [1] 2 uvrB excinulease of nucleotide excision repair, DNA damage recognition component
* * ÷ minE 543250 543260 11 2 [1] [1] 2 ybiP predicted hydrolase, inner membrane
* * ÷ minE 549556 549584 29 2 [1] [1] 2 ybiU hypothetical protein
* * ÷ minE 558161 558197 37 2 [1] [1] 2 iaaA L‑asparaginase
* * ÷ minE 567842 567850 9 2 [0] [1] 2 poxB/hcr pyruvate dehydrogenase (pyruvate oxidase), thiamin‑dependent, FAD‑binding/HCP oxidoreductase, NADH‑dependent
* * ÷ minE 571858 571910 53 2 [1] [1] 2 ybjE/aqpZ predicted transporter/aquaporin
* * ÷ minE 582688 582717 30 2 [1] [1] 2 serW/infA tRNA‑Ser/translation initiation factor IF‑1
* * ÷ minE 649955 649980 26 2 [1] [1] 2 [ssuB] [ssuB]
* * ÷ minE 662450 662479 30 2 [1] [1] 2 [pyrD] [pyrD]
* * ÷ minE 667178 667202 25 2 [1] [1] 2 uup fused predicted transporter subunits and ATP‑binding components of ABC superfamily
* * ÷ minE 698167 698193 27 3 [1] [1] 3 appA phosphoanhydride phosphorylase
* * ÷ minE 713933 713951 19 3 [1] [1] 2 yceB predicted lipoprotein
* * ÷ minE 750850 750886 37 2 [1] [1] 2 mfd transcription‑repair coupling factor
* * ÷ minE 755789 755801 13 2 [1] [1] 2 lolC outer membrane‑specific lipoprotein transporter subunit
* * ÷ minE 772988 773018 31 2 [1] [1] 2 trmU tRNA (5‑methylaminomethyl‑2‑thiouridylate)‑methyltransferase
* * ÷ minE 782546 782566 21 2 [1] [1] 2 hlyE hemolysin E
* * ÷ minE 814541 814575 35 2 [1] [1] 3 ispE 4‑diphosphocytidyl‑2‑C‑methylerythritol kinase
* * ÷ minE 833129 833136 8 2 [1] [1] 2 narG nitrate reductase 1, alpha subunit
* * ÷ minE 859350 859375 26 2 [1] [1] 2 trpD fused glutamine amidotransferase (component II) of anthranilate synthase and anthranilate phosphoribosyl transferase
* * ÷ minE 865558 865591 34 2 [1] [1] 2 yciQ predicted inner membrane protein
* * ÷ minE 875450 875476 27 2 [1] [1] 2 acnA aconitate hydratase 1
* * ÷ minE 885820 885852 33 2 [1] [1] 4 gmr/rnb modulator of Rnase II stability/ribonuclease II
* * ÷ minE 899423 899466 44 2 [1] [1] 2 pspD peripheral inner membrane phage‑shock protein
* * ÷ minE 906887 906930 44 2 [1] [1] 2 ycjS predicted oxidoreductase, NADH‑binding
* * ÷ minE 908995 909028 34 2 [1] [1] 2 ycjT predicted hydrolase
* * ÷ minE 944003 944006 4 3 [0] [1] 2 ddpD D‑Ala‑D‑Ala transporter subunit
* * ÷ minE 1000458 1000491 34 3 [1] [1] 2 [ydgD] [ydgD]
* * ÷ minE 1069378 1069407 30 2 [0] [1] 2 cfa cyclopropane fatty acyl phospholipid synthase
* * ÷ minE 1119914 1119939 26 2 [1] [1] 2 ydiV/nlpC conserved hypothetical protein/predicted lipoprotein
* * ÷ minE 1122549 1122567 19 2 [1] [1] 3 btuC vitamin B12 transporter subunit
* * ÷ minE 1148191 1148213 23 2 [1] [1] 2 chbC N,N'‑diacetylchitobiose‑specific enzyme IIC component of PTS
* * ÷ minE 1154056 1154101 46 2 [1] [1] 3 astE succinylglutamate desuccinylase
* * ÷ minE 1156073 1156092 20 2 [1] [1] 2 astD succinylglutamic semialdehyde dehydrogenase
* * ÷ minE 1181880 1181901 22 2 [0] [0] 2 yeaD/yeaE conserved hypothetical protein/predicted oxidoreductase
* * ÷ minE 1231150 1231163 14 2 [1] [0] 2 ptrB protease II
* * ÷ minE 1309237 1309267 31 2 [1] [1] 2 yeeZ predicted epimerase, with NAD(P)‑binding Rossmann‑fold domain
* * ÷ minE 1312127 1312147 21 2 [1] [1] 2 hisD bifunctional histidinal dehydrogenase and histidinol dehydrogenase
* * ÷ minE 1329606 1329631 26 2 [1] [0] 2 wcaJ predicted UDP‑glucose lipid carrier transferase
* * ÷ minE 1407035 1407059 25 2 [1] [1] 3 yejE predicted oligopeptide transporter subunit
* * ÷ minE 1420603 1420616 14 2 [1] [1] 2 ccmF heme lyase, CcmF subunit
* * ÷ minE 1442363 1442376 14 2 [1] [1] 2 rcsD phosphotransfer intermediate protein in two‑component regulatory system with RcsBC
* * ÷ minE 1449980 1450008 29 2 [1] [1] 3 atoC fused response regulator of ato opeon, in two‑component system with AtoS
* * ÷ minE 1461194 1461216 23 2 [1] [1] 2 yfaS
yfaS		 ECK2220:JW2222+JW2221:b4500; hypothetical protein
ECK2220:JW2222:b2228; hypothetical protein, N‑ter fragment
* * ÷ minE 1564325 1564342 18 2 [1] [1] 3 yfdE predicted CoA‑transferase, NAD(P)‑binding
* * ÷ minE 1584648 1584679 32 2 [1] [1] 2 cysZ predicted inner membrane protein
* * ÷ minE 1589419 1589425 7 2 [1] [0] 2 crr/pdxK glucose‑specific enzyme IIA component of PTS/pyridoxal‑pyridoxamine kinase/hydroxymethylpyrimidine kinase
* * ÷ minE 1613055 1613083 29 2 [1] [1] 3 eutA reactivating factor for ethanolamine ammonia lyase
* * ÷ minE 1616711 1616755 45 2 [1] [1] 2 eutE predicted aldehyde dehydrogenase, ethanolamine utilization protein
* * ÷ minE 1618895 1618906 12 2 [1] [1] 2 eutI predicted phosphotransacetylase subunit
* * ÷ minE 1655666 1655673 8 2 [1] [1] 3 purN/ppk phosphoribosylglycinamide formyltransferase 1/polyphosphate kinase, component of RNA degradosome
* * ÷ minE 1665306 1665317 12 2 [1] [1] 2 guaB IMP dehydrogenase
* * ÷ minE 1669758 1669770 13 2 [1] [1] 2 der predicted GTP‑binding protein
* * ÷ minE 1679380 1679403 24 2 [1] [1] 2 pbpC fused transglycosylase and transpeptidase
* * ÷ minE 1711446 1711449 4 2 [1] [1] 2 yphF predicted sugar transporter subunit
* * ÷ minE 1757018 1757046 29 2 [1] [1] 2 yfiM hypothetical protein
* * ÷ minE 1781760 1781798 39 2 [1] [1] 2 yfjD predicted inner membrane protein
* * ÷ minE 1817914 1817921 8 2 [1] [1] 2 mltB membrane‑bound lytic murein transglycosylase B
* * ÷ minE 1847538 1847608 71 2 [1] [1] 2 iap/ygbF aminopeptidase in alkaline phosphatase isozyme conversion/hypothetical protein
* * ÷ minE 1847680 1847741 62 2 [1] [1] 2 iap/ygbF aminopeptidase in alkaline phosphatase isozyme conversion/hypothetical protein
* * ÷ minE 1857049 1857086 38 2 [1] [1] 2 [cysH] [cysH]
* * ÷ minE 1888237 1888272 36 2 [1] [1] 2 gudD (D)‑glucarate dehydratase 1
* * ÷ minE 1902485 1902509 25 2 [1] [1] 2 recB exonuclease V (RecBCD complex), beta subunit
* * ÷ minE 1945301 1945331 31 2 [1] [1] 2 ygfF/gcvP predicted NAD(P)‑binding oxidoreductase with NAD(P)‑binding Rossmann‑fold domain/glycine decarboxylase, PLP‑dependent, subunit (protein P) of glycine cleavage complex
* * ÷ minE 1975622 1975665 44 2 [1] [1] 2 galP D‑galactose transporter
* * ÷ minE 2032061 2032083 23 2 [1] [1] 2 cpdA cyclic 3',5'‑adenosine monophosphate phosphodiesterase
* * ÷ minE 2095579 2095609 31 2 [1] [1] 2 rnpB RNase P
* * ÷ minE 2101428 2101442 15 2 [1] [1] 2 garD (D)‑galactarate dehydrogenase
* * ÷ minE 2117659 2117684 26 2 [1] [1] 2 yraL predicted methyltransferase
* * ÷ minE 2157998 2158012 15 2 [1] [1] 2 rpmA 50S ribosomal subunit protein L27
* * ÷ minE 2222578 2222592 15 2 [1] [1] 2 accC/yhdT acetyl‑CoA carboxylase, biotin carboxylase subunit/conserved inner membrane protein
* * ÷ minE 2223103 2223119 17 2 [0] [1] 3 panF pantothenate:sodium symporter
* * ÷ minE 2238150 2238179 30 2 [1] [1] 2 zraR fused DNA‑binding response regulator in two‑component regulatory system with ZraS
* * ÷ minE 2335643 2335678 36 3 [1] [1] 5 fdoH formate dehydrogenase‑O, Fe‑S subunit
* * ÷ minE 2415802 2415828 27 2 [1] [1] 2 proM tRNA‑Pro
* * ÷ minE 2420928 2420947 20 2 [1] [1] 2 rffT TDP‑Fuc4NAc:lipidII transferase
* * ÷ minE 2502763 2502775 13 2 [1] [1] 2 uhpC membrane protein regulates uhpT expression
* * ÷ minE 2573773 2573827 55 2 [1] [1] 2 glyQ glycine tRNA synthetase, alpha subunit
* * ÷ minE 2627312 2627319 8 2 [1] [0] 2 rpoH/livJ RNA polymerase, sigma 32 (sigma H) factor/leucine/isoleucine/valine transporter subunit
* * ÷ minE 2655026 2655044 19 2 [1] [0] 2 glgP glycogen phosphorylase
* * ÷ minE 2664433 2664474 42 2 [1] [1] 2 rtcA RNA 3'‑terminal phosphate cyclase
* * ÷ minE 2664545 2664660 116 2 [1] [1] 2 rtcA RNA 3'‑terminal phosphate cyclase
* * ÷ minE 2731387 2731412 26 2 [1] [1] 2 fkpA FKBP‑type peptidyl‑prolyl cis‑trans isomerase
* * ÷ minE 2824193 2824202 10 2 [1] [1] 2 nrfG/pheU heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfG/tRNA‑Phe
* * ÷ minE 2840625 2840650 26 2 [1] [1] 2 ampC/frdD beta‑lactamase/D‑alanine carboxypeptidase/fumarate reductase (anaerobic), membrane anchor subunit
* * ÷ minE 2858105 2858155 51 2 [1] [1] 2 amiB N‑acetylmuramoyl‑l‑alanine amidase II
* * ÷ minE 2906519 2906537 19 2 [0] [1] 2 treB fused trehalose(maltose)‑specific enzyme IIBC component of PTS
* * ÷ minE 2945538 2945561 24 3 [0] [1] 2 fecR transmembrane signal transducer for ferric citrate transport

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? minE = 43683319 (2.100)11 (1.220) 8/108 NT 43.1% coding (546/546 nt) seqA regulatory protein for replication initiation
?minE 1803907 = 10 (1.110)intergenic (+63/‑28) ygaH/mprA predicted inner membrane protein/DNA‑binding transcriptional regulator