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 1,036,505 G→A 100% A632A (GCG→GCA)  rsxC → fused predicted 4Fe‑4S ferredoxin‑type protein
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 35.0% noncoding (1228/2905 nt) rrlA ← 23S ribosomal RNA
RA 2,359,876 C→T 31.8% noncoding (1219/2905 nt) rrlA ← 23S ribosomal RNA

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ Exported 5448 5475 28 2 [1] [1] 2 yaaX hypothetical protein
* * ÷ Exported 16632 16647 16 2 [1] [1] 3 nhaA sodium‑proton antiporter
* * ÷ Exported 23439 23455 17 2 [1] [1] 2 lspA/fkpB prolipoprotein signal peptidase/FKBP‑type peptidyl‑prolyl cis‑trans isomerase
* * ÷ Exported 64281 64297 17 2 [0] [1] 2 leuC 3‑isopropylmalate isomerase subunit, dehydratase component
* * ÷ Exported 64498 64515 18 2 [1] [1] 2 leuC 3‑isopropylmalate isomerase subunit, dehydratase component
* * ÷ Exported 85225 85265 41 2 [1] [1] 2 murG N‑acetylglucosaminyl transferase
* * ÷ Exported 111012 111042 31 2 [1] [1] 2 aceF pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2
* * ÷ Exported 149304 149345 42 2 [1] [1] 2 hrpB/mrcB predicted ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
* * ÷ Exported 167491 167518 28 2 [1] [1] 2 glnD/map uridylyltransferase/methionine aminopeptidase
* * ÷ Exported 170548 170577 30 2 [1] [1] 2 tsf/pyrH protein chain elongation factor EF‑Ts/uridylate kinase
* * ÷ Exported 193418 193449 32 3 [1] [1] 2 yaeQ conserved hypothetical protein
* * ÷ Exported 193914 193942 29 2 [1] [1] 2 yaeJ conserved hypothetical protein
* * ÷ Exported 222593 222628 36 2 [1] [1] 2 lpcA D‑sedoheptulose 7‑phosphate isomerase
* * ÷ Exported 252010 252043 34 2 [1] [1] 2 malZ maltodextrin glucosidase
* * ÷ Exported 288431 288444 14 2 [1] [1] 2 lon DNA‑binding ATP‑dependent protease La
* * ÷ Exported 304423 304453 31 2 [0] [0] 2 [ybaZ] [ybaZ]
* * ÷ Exported 321883 321967 85 2 [1] [1] 2 dnaX DNA polymerase III/DNA elongation factor III, tau and gamma subunits
* * ÷ Exported 329937 329960 24 2 [1] [1] 2 gsk/ybaL inosine/guanosine kinase/predicted transporter with NAD(P)‑binding Rossmann‑fold domain
* * ÷ Exported 339144 339181 38 2 [1] [1] 2 copA copper transporter
* * ÷ Exported 341116 341157 42 2 [1] [1] 2 ybaT predicted transporter
* * ÷ Exported 343160 343178 19 2 [1] [1] 2 ybbJ conserved inner membrane protein
* * ÷ Exported 377736 377765 30 2 [1] [1] 2 ybdA predicted transporter
* * ÷ Exported 394542 394553 12 2 [1] [1] 2 ahpC/ahpF alkyl hydroperoxide reductase, C22 subunit/alkyl hydroperoxide reductase, F52a subunit, FAD/NAD(P)‑binding
* * ÷ Exported 396315 396339 25 2 [1] [1] 2 ahpF/ybeM alkyl hydroperoxide reductase, F52a subunit, FAD/NAD(P)‑binding/predicted C‑N hydrolase superfamily, NAD(P)‑binding amidase/nitrilase
* * ÷ Exported 409120 409155 36 2 [1] [1] 3 holA DNA polymerase III, delta subunit
* * ÷ Exported 417116 417142 27 2 [1] [1] 2 miaB isopentenyl‑adenosine A37 tRNA methylthiolase
* * ÷ Exported 431230 431277 48 2 [1] [0] 2 glnS/ybfM glutamyl‑tRNA synthetase/predicted outer membrane porin
* * ÷ Exported 432316 432334 19 3 [1] [1] 2 ybfM predicted outer membrane porin
* * ÷ Exported 444353 444445 93 3 [1] [1] 2 [kdpE] [kdpE]
* * ÷ Exported 447388 447444 57 2 [1] [1] 2 kdpD fused sensory histidine kinase in two‑component regulatory system with KdpE
* * ÷ Exported 480816 480828 13 2 [1] [1] 2 ybgE conserved inner membrane protein
* * ÷ Exported 483540 483712 173 2 [1] [1] 2 tolA membrane anchored protein in TolA‑TolQ‑TolR complex
* * ÷ Exported 497399 497456 58 2 [1] [1] 2 galT galactose‑1‑phosphate uridylyltransferase
* * ÷ Exported 514529 514565 37 2 [1] [1] 2 bioA 7,8‑diaminopelargonic acid synthase, PLP‑dependent
* * ÷ Exported 525521 525545 25 2 [1] [1] 2 moaD molybdopterin synthase, small subunit
* * ÷ Exported 538706 538720 15 2 [1] [1] 3 rhlE/dps RNA helicase/Fe‑binding and storage protein
* * ÷ Exported 546116 546163 48 2 [1] [1] 2 ybiS conserved hypothetical protein
* * ÷ Exported 562930 562942 13 2 [1] [1] 2 ybjK predicted DNA‑binding transcriptional regulator
* * ÷ Exported 566703 566721 19 2 [1] [1] 2 poxB pyruvate dehydrogenase (pyruvate oxidase), thiamin‑dependent, FAD‑binding
* * ÷ Exported 571862 571921 60 2 [1] [1] 2 ybjE/aqpZ predicted transporter/aquaporin
* * ÷ Exported 577266 577289 24 2 [1] [1] 2 macB fused macrolide transporter subunits and ATP‑binding component and membrane component of ABC superfamily
* * ÷ Exported 597447 597474 28 2 [1] [1] 3 serS/dmsA seryl‑tRNA synthetase, also charges selenocysteinyl‑tRNA with serine/dimethyl sulfoxide reductase, anaerobic, subunit A
* * ÷ Exported 647577 647605 29 2 [1] [1] 2 pepN aminopeptidase N
* * ÷ Exported 658288 658335 48 2 [1] [1] 3 ycbS predicted outer membrane usher protein
* * ÷ Exported 698176 698199 24 2 [1] [1] 2 appA phosphoanhydride phosphorylase
* * ÷ Exported 705619–705730 705740 11–122 2 [1] [1] 2 ymcC/serX predicted outer membrane lipoprotein/tRNA‑Ser
* * ÷ Exported 712005 712048 44 2 [0] [1] 2 yceP/dinI hypothetical protein/DNA damage‑inducible protein I
* * ÷ Exported 725195 725214 20 2 [1] [0] 2 rluC/yceF 23S rRNA pseudouridylate synthase/hypothetical protein
* * ÷ Exported 750863 750893 31 2 [1] [1] 2 mfd transcription‑repair coupling factor
* * ÷ Exported 752122 752154 33 2 [1] [1] 2 mfd transcription‑repair coupling factor
* * ÷ Exported 752225 752266 42 2 [0] [1] 2 mfd transcription‑repair coupling factor
* * ÷ Exported 833586 833608 23 3 [1] [1] 2 narG nitrate reductase 1, alpha subunit
* * ÷ Exported 850795 850809 15 2 [1] [1] 3 [yciA] [yciA]
* * ÷ Exported 865558 865585 28 2 [1] [1] 2 yciQ predicted inner membrane protein
* * ÷ Exported 875447 875461 15 2 [1] [0] 2 acnA aconitate hydratase 1
* * ÷ Exported 899406 899451 46 2 [1] [1] 3 pspD peripheral inner membrane phage‑shock protein
* * ÷ Exported 911156 911194 39 2 [1] [1] 2 ycjV predicted sugar transporter subunit
* * ÷ Exported 914817 914842 26 3 [1] [1] 2 ycjX conserved hypothetical protein with nucleoside triphosphate hydrolase domain
* * ÷ Exported 924005 924016 12 2 [1] [1] 3 mppA murein tripeptide (L‑ala‑gamma‑D‑glutamyl‑meso‑DAP) transporter subunit
* * ÷ Exported 1030820 1030838 19 2 [1] [1] 2 add adenosine deaminase
* * ÷ Exported 1033877 1033895 19 3 [1] [1] 2 rsxA predicted inner membrane subunit
* * ÷ Exported 1034694 1034733 40 2 [1] [1] 2 rsxC fused predicted 4Fe‑4S ferredoxin‑type protein
* * ÷ Exported 1037737 1037743 7 2 [1] [0] 2 rsxD predicted inner membrane oxidoreductase
* * ÷ Exported 1046307 1046317 11 3 [1] [1] 3 ydhH conserved hypothetical protein
* * ÷ Exported 1048053 1048061 9 2 [1] [1] 2 slyB/slyA outer membrane lipoprotein/DNA‑binding transcriptional activator
* * ÷ Exported 1056849 1056895 47 2 [1] [1] 3 lhr predicted ATP‑dependent helicase
* * ÷ Exported 1056967 1057000 34 2 [0] [1] 2 lhr predicted ATP‑dependent helicase
* * ÷ Exported 1092390 1092431 42 2 [1] [1] 2 sufA/ydiH Fe‑S cluster assembly protein/hypothetical protein
* * ÷ Exported 1103147 1103153 7 2 [1] [1] 2 aroD/ydiF 3‑dehydroquinate dehydratase/fused predicted acetyl‑CoA:acetoacetyl‑CoA transferase: alpha subunit and beta subunit
* * ÷ Exported 1154060 1154102 43 2 [1] [1] 2 astE succinylglutamate desuccinylase
* * ÷ Exported 1157036 1157056 21 2 [1] [1] 3 astD succinylglutamic semialdehyde dehydrogenase
* * ÷ Exported 1208802 1208804 3 2 [1] [0] 2 yobD conserved inner membrane protein
* * ÷ Exported 1231134 1231164 31 2 [1] [1] 2 ptrB protease II
* * ÷ Exported 1249836 1249855 20 3 [1] [0] 2 ruvA component of RuvABC resolvasome, regulatory subunit
* * ÷ Exported 1279183 1279198 16 2 [1] [1] 2 yeeJ adhesin
* * ÷ Exported 1292330 1292381 52 2 [1] [1] 2 yeeO predicted multidrug efflux system
* * ÷ Exported 1309183 1309209 27 2 [1] [1] 2 yeeZ predicted epimerase, with NAD(P)‑binding Rossmann‑fold domain
* * ÷ Exported 1320080 1320102 23 2 [1] [1] 2 ugd/gnd UDP‑glucose 6‑dehydrogenase/gluconate‑6‑phosphate dehydrogenase, decarboxylating
* * ÷ Exported 1368198 1368281 84 2 [1] [1] 2 yohH/dusC conserved hypothetical protein/tRNA‑dihydrouridine synthase C
* * ÷ Exported 1374845 1374875 31 3 [1] [1] 2 yeiA predicted oxidoreductase
* * ÷ Exported 1391544 1391564 21 2 [1] [1] 3 fruA fused fructose‑specific PTS enzyme IIB'BC components
* * ÷ Exported 1414249 1414282 34 2 [1] [1] 2 rplY/yejK 50S ribosomal subunit protein L25/nucleotide associated protein
* * ÷ Exported 1420600 1420649 50 2 [1] [1] 2 ccmF heme lyase, CcmF subunit
* * ÷ Exported 1427679 1427700 22 2 [1] [1] 2 napG ferredoxin‑type protein essential for electron transfer from ubiquinol to periplasmic nitrate reductase (NapAB)
* * ÷ Exported 1432594 1432635 42 2 [1] [1] 2 eco/mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
* * ÷ Exported 1433461 1433480 20 2 [1] [1] 2 mqo malate dehydrogenase, FAD/NAD(P)‑binding domain
* * ÷ Exported 1527549 1527567 19 3 [1] [1] 2 trmC fused 5‑methylaminomethyl‑2‑thiouridine forming enzyme methyltransferase and FAD‑dependent demodification enzyme
* * ÷ Exported 1527875 1527919 45 2 [1] [1] 2 trmC fused 5‑methylaminomethyl‑2‑thiouridine forming enzyme methyltransferase and FAD‑dependent demodification enzyme
* * ÷ Exported 1593429 1593446 18 2 [1] [1] 3 cysA sulfate/thiosulfate transporter subunit
* * ÷ Exported 1608244 1608270 27 2 [1] [1] 2 yfeG/yffI predicted DNA‑binding transcriptional regulator/predicted carboxysome structural protein with predicted role in ethanolamine utilization
* * ÷ Exported 1616720 1616744 25 2 [1] [1] 2 eutE predicted aldehyde dehydrogenase, ethanolamine utilization protein
* * ÷ Exported 1658268 1658306 39 3 [1] [1] 2 ppx exopolyphosphatase
* * ÷ Exported 1703980 1703991 12 2 [1] [0] 2 hcaB 2,3‑dihydroxy‑2,3‑dihydrophenylpropionate dehydrogenase
* * ÷ Exported 1718372 1718377 6 2 [0] [1] 2 glyA/hmp serine hydroxymethyltransferase/fused nitric oxide dioxygenase and dihydropteridine reductase 2
* * ÷ Exported 1727267 1727320 54 2 [1] [1] 3 purL phosphoribosylformyl‑glycineamide synthetase
* * ÷ Exported 1736985 1736992 8 2 [1] [1] 2 rnc/lepB RNase III/leader peptidase
* * ÷ Exported 1751269 1751281 13 2 [1] [1] 3 yfiF/trxC predicted methyltransferase/thioredoxin 2
* * ÷ Exported 1766135 1766165 31 2 [1] [1] 2 clpB protein disaggregation chaperone
* * ÷ Exported 1788677 1788712 36 2 [1] [1] 2 smpB/ygaF trans‑translation protein/hypothetical protein
* * ÷ Exported 1789863 1789878 16 2 [1] [1] 2 ygaF hypothetical protein
* * ÷ Exported 1790615 1790675 61 2 [1] [1] 2 gabD succinate‑semialdehyde dehydrogenase I, NADP‑dependent
* * ÷ Exported 1791851 1791855 5 2 [1] [0] 2 gabT 4‑aminobutyrate aminotransferase, PLP‑dependent
* * ÷ Exported 1792922 1792967 46 2 [1] [1] 2 gabT/gabP 4‑aminobutyrate aminotransferase, PLP‑dependent/gamma‑aminobutyrate transporter
* * ÷ Exported 1808044 1808079 36 2 [1] [1] 2 [gshA] [gshA]
* * ÷ Exported 1825827 1825840 14 2 [1] [0] 2 hydN formate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit
* * ÷ Exported 1847469 1847503 35 2 [1] [1] 2 iap/ygbF aminopeptidase in alkaline phosphatase isozyme conversion/hypothetical protein
* * ÷ Exported 1847573 1847653 81 2 [1] [1] 2 iap/ygbF aminopeptidase in alkaline phosphatase isozyme conversion/hypothetical protein
* * ÷ Exported 1847743 1847947 205 2 [1] [1] 2 iap/ygbF aminopeptidase in alkaline phosphatase isozyme conversion/hypothetical protein
* * ÷ Exported 1864676 1864772 97 2 [0] [1] 2 ygcQ predicted flavoprotein
* * ÷ Exported 1873551 1873587 37 2 [1] [1] 2 ygcE/ygcF predicted kinase/conserved hypothetical protein
* * ÷ Exported 1873637 1873705 69 2 [1] [1] 2 ygcE/ygcF predicted kinase/conserved hypothetical protein
* * ÷ Exported 1873744 1873829 86 2 [1] [1] 2 ygcE/ygcF predicted kinase/conserved hypothetical protein
* * ÷ Exported 1876016 1876104 89 2 [1] [1] 2 [ygcG] [ygcG]
* * ÷ Exported 1898891 1898927 37 2 [1] [1] 2 recD exonuclease V (RecBCD complex), alpha chain
* * ÷ Exported 1899058 1899063 6 3 [1] [1] 2 recD exonuclease V (RecBCD complex), alpha chain
* * ÷ Exported 1945277 1945325 49 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
* * ÷ Exported 1988024 1988043 20 2 [1] [1] 2 yggN hypothetical protein
* * ÷ Exported 2056679 2056693 15 2 [1] [1] 2 ygiP predicted DNA‑binding transcriptional regulator
* * ÷ Exported 2056867 2056884 18 2 [1] [1] 2 ygiP predicted DNA‑binding transcriptional regulator
* * ÷ Exported 2060626 2060657 32 2 [1] [1] 2 ygjD predicted peptidase
* * ÷ Exported 2095558 2095600 43 2 [1] [1] 3 rnpB RNase P
* * ÷ Exported 2142054 2142081 28 2 [1] [0] 2 nusA transcription termination/antitermination L factor
* * ÷ Exported 2156403 2156413 11 2 [1] [1] 2 obgE GTPase involved in cell partioning and DNA repair
* * ÷ Exported 2183099 2183118 20 2 [1] [1] 2 gltB glutamate synthase, large subunit
* * ÷ Exported 2221675 2221711 37 2 [1] [1] 2 accC acetyl‑CoA carboxylase, biotin carboxylase subunit
* * ÷ Exported 2228829 2228951 123 2 [1] [1] 2 yhdZ/rrfF predicted amino‑acid transporter subunit/5S ribosomal RNA
* * ÷ Exported 2270442 2270576–2270449 8–135 4 [1] [1] 2 murB/rrfB UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding/5S ribosomal RNA
* * ÷ Exported 2280223 2280236 14 2 [1] [0] 3 trmA/yijD tRNA (uracil‑5‑)‑methyltransferase/conserved inner membrane protein
* * ÷ Exported 2342558 2342582 25 3 [1] [1] 2 glnL sensory kinase in two‑component regulatory system with GlnG
* * ÷ Exported 2345031 2345064 34 2 [1] [1] 2 glnG/hemN fused DNA‑binding response regulator in two‑component regulatory system with GlnL, nitrogen regulator I (NRI)/coproporphyrinogen III oxidase, SAM and NAD(P)H dependent, oxygen‑independent
* * ÷ Exported 2354509 2354521 13 2 [0] [1] 2 yihF/dsbA conserved hypothetical protein/periplasmic protein disulfide isomerase I
* * ÷ Exported 2504513 2504535 23 2 [1] [1] 2 uhpT/selC hexose phosphate transporter/tRNA‑Sec
* * ÷ Exported 2530228 2530265 38 2 [1] [1] 2 rpmG/mutM 50S ribosomal subunit protein L33/formamidopyrimidine/5‑formyluracil/ 5‑hydroxymethyluracil DNA glycosylase
* * ÷ Exported 2560327 2560361 35 2 [0] [1] 2 yibK/lldD predicted rRNA methylase/L‑lactate dehydrogenase, FMN‑linked
* * ÷ Exported 2560396 2560420 25 2 [1] [1] 2 yibK/lldD predicted rRNA methylase/L‑lactate dehydrogenase, FMN‑linked
* * ÷ Exported 2604939 2604960 22 2 [0] [1] 4 yhiP/uspA predicted transporter/universal stress global response regulator
* * ÷ Exported 2607325 2607353 29 2 [1] [1] 2 pitA phosphate transporter, low‑affinity
* * ÷ Exported 2608946 2608972 27 2 [0] [1] 4 nikE nickel transporter subunit
* * ÷ Exported 2609209 2609258 50 2 [1] [1] 2 nikE nickel transporter subunit
* * ÷ Exported 2610003 2610042 40 2 [1] [1] 3 nikD nickel transporter subunit
* * ÷ Exported 2613619 2613631 13 2 [1] [1] 2 nikA/acpT nickel transporter subunit/holo‑(acyl carrier protein) synthase 2
* * ÷ Exported 2618452 2618479 28 2 [1] [1] 2 yhhP/zntA conserved hypothetical protein required for cell growth/zinc, cobalt and lead efflux system
* * ÷ Exported 2635360 2635420 61 2 [1] [1] 2 ugpB glycerol‑3‑phosphate transporter subunit
* * ÷ Exported 2664452 2664472 21 2 [1] [1] 2 rtcA RNA 3'‑terminal phosphate cyclase
* * ÷ Exported 2725751 2725805 55 2 [1] [1] 2 yheS fused predicted transporter subunits and ATP‑binding components of ABC superfamily
* * ÷ Exported 2731782 2731823 42 3 [0] [1] 2 fkpA/yheO FKBP‑type peptidyl‑prolyl cis‑trans isomerase/predicted DNA‑binding transcriptional regulator
* * ÷ Exported 2753665 2753682 18 3 [1] [1] 2 mscL mechanosensitive channel
* * ÷ Exported 2840627 2840638 12 3 [1] [0] 2 ampC/frdD beta‑lactamase/D‑alanine carboxypeptidase/fumarate reductase (anaerobic), membrane anchor subunit
* * ÷ Exported 2858097 2858126 30 2 [1] [1] 2 amiB N‑acetylmuramoyl‑l‑alanine amidase II
* * ÷ Exported 2858655 2858688 34 2 [1] [1] 2 amiB N‑acetylmuramoyl‑l‑alanine amidase II
* * ÷ Exported 2860489 2860508 20 4 [1] [1] 2 mutL methyl‑directed mismatch repair protein
* * ÷ Exported 2913818 2913836 19 3 [1] [1] 2 pyrL pyrBI operon leader peptide
* * ÷ Exported 2920401 2920443 43 2 [1] [1] 5 [yjgM] [yjgM]
* * ÷ Exported 2973407 2973418 12 2 [0] [1] 2 radA predicted repair protein

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? Exported 1611749 =1 (0.100)6 (0.680)
+ATGCGGT		 5/86 NT 69.9% coding (1404/1404 nt) eutA reactivating factor for ethanolamine ammonia lyase
?Exported = 2603083 5 (0.490)coding (684/753 nt) yhiQ predicted SAM‑dependent methyltransferase