breseq  version 0.35.4  revision f352f80f4bc9
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% insB9–[crl] insB9, insA9, [crl]
RA 880,492 T→C 28.7% intergenic (‑12/‑235) gstB ← / → dacC glutathione S‑transferase GstB/D‑alanyl‑D‑alanine carboxypeptidase DacC
MC JC 1,299,499 Δ1,199 bp 100% insH21 insH21
RA 1,395,649 T→C 17.4% I92V (ATT→GTT)  ynaI ← small conductance mechanosensitive channel YnaI
RA 1,818,531 T→A 12.5% intergenic (‑31/+74) chbF ← / ← chbR monoacetylchitobiose‑6‑phosphate hydrolase/ChbR
MC JC 1,978,503 Δ776 bp 100% insB5–insA5 insB5, insA5
JC JC 1,979,486 IS5 (+) +4 bp 100% intergenic (‑271/‑264) insA5 ← / → uspC IS1 family protein InsA/universal stress protein C
RA 2,173,361 Δ2 bp 100% intergenic (‑488/+920) gatD ← / ← gatB galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component
RA 2,239,405 Δ1 bp 12.9% coding (944/999 nt) mglB ← D‑galactose/methyl‑galactoside ABC transporter periplasmic binding protein
RA 2,993,470 A→T 9.0% *459Y (TAA→TAT)  ygeH → putative transcriptional regulator YgeH
RA 3,071,836 A→G 27.4% F263L (TTC→CTC)  pgk ← phosphoglycerate kinase
RA 3,560,455:1 +G 100% intergenic (+589/+167) rtcR → / ← glpG DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG
RA 4,000,980 A→T 13.9% L26H (CTT→CAT)  yigE ← DUF2233 domain‑containing protein YigE
RA 4,186,578 A→T 100% D410V (GAT→GTT)  rpoC → RNA polymerase subunit beta'
RA 4,296,060 C→T 28.0% intergenic (+266/+376) gltP → / ← yjcO glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
RA 4,296,380:1 +CG 100% intergenic (+586/+56) gltP → / ← yjcO glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
RA 4,466,422 C→T 17.5% P275P (CCG→CCA)  treR ← DNA‑binding transcriptional repressor TreR

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 3571 3617 47 2 [1] [1] 2 thrB homoserine kinase
* * ÷ NC_000913 79528 79568 41 2 [0] [1] 2 leuC 3‑isopropylmalate dehydratase subunit LeuC
* * ÷ NC_000913 162246 162327 82 2 [1] [1] 2 hrpB RNA‑dependent NTPase HrpB
* * ÷ NC_000913 172498 172547 50 2 [1] [1] 2 fhuB iron(III) hydroxamate ABC transporter membrane subunit
* * ÷ NC_000913 172617 172626 10 2 [1] [1] 2 fhuB iron(III) hydroxamate ABC transporter membrane subunit
* * ÷ NC_000913 281136 281277 142 2 [0] [1] 2 yagA integrase core domain‑containing protein YagA
* * ÷ NC_000913 281537 281816 280 2 [1] [1] 2 yagA integrase core domain‑containing protein YagA
* * ÷ NC_000913 282458 282602 145 2 [1] [1] 2 yagE putative 2‑dehydro‑3‑deoxygluconate aldolase
* * ÷ NC_000913 283093 283163 71 2 [1] [1] 2 yagE putative 2‑dehydro‑3‑deoxygluconate aldolase
* * ÷ NC_000913 283443 284048 606 2 [1] [1] 2 yagF D‑xylonate dehydratase
* * ÷ NC_000913 284218 284465 248 3 [1] [1] 2 yagF D‑xylonate dehydratase
* * ÷ NC_000913 284824 285031 208 2 [1] [0] 2 yagF D‑xylonate dehydratase
* * ÷ NC_000913 285536 285701 166 2 [0] [1] 2 yagG putative D‑xylonate transporter YagG
* * ÷ NC_000913 285773 285961 189 2 [1] [1] 2 yagG putative D‑xylonate transporter YagG
* * ÷ NC_000913 287584 287862 279 2 [1] [1] 2 yagH putative xylosidase/arabinosidase
* * ÷ NC_000913 288323 288425 103 2 [1] [1] 2 [yagH]–[xynR] [yagH],[xynR]
* * ÷ NC_000913 288486 288631 146 2 [1] [1] 2 xynR DNA‑binding transcriptional repressor XynR
* * ÷ NC_000913 288726 288748 23 2 [1] [1] 2 xynR DNA‑binding transcriptional repressor XynR
* * ÷ NC_000913 289754 289764 11 2 [0] [1] 2 argF ornithine carbamoyltransferase ArgF
* * ÷ NC_000913 289820 289912 93 2 [1] [1] 2 argF ornithine carbamoyltransferase ArgF
* * ÷ NC_000913 299666 299679 14 2 [0] [1] 2 paoC aldehyde dehydrogenase: molybdenum cofactor‑binding subunit
* * ÷ NC_000913 299855 299898 44 2 [0] [1] 2 paoC aldehyde dehydrogenase: molybdenum cofactor‑binding subunit
* * ÷ NC_000913 300050 300073 24 3 [0] [1] 2 paoC aldehyde dehydrogenase: molybdenum cofactor‑binding subunit
* * ÷ NC_000913 301099 301181 83 5 [1] [1] 2 paoB aldehyde dehydrogenase, FAD‑binding subunit
* * ÷ NC_000913 301549 301693 145 2 [1] [1] 2 paoB aldehyde dehydrogenase, FAD‑binding subunit
* * ÷ NC_000913 326587 326647 61 2 [1] [1] 2 betA choline dehydrogenase
* * ÷ NC_000913 339246 339342 97 2 [1] [1] 2 yahG DUF1116 domain‑containing protein YahG
* * ÷ NC_000913 351548 351647 100 2 [1] [1] 2 prpD 2‑methylcitrate dehydratase
* * ÷ NC_000913 353343 353376 34 2 [1] [1] 2 prpE propionyl‑CoA synthetase
* * ÷ NC_000913 353409 353431 23 2 [1] [1] 2 prpE propionyl‑CoA synthetase
* * ÷ NC_000913 473818 473862 45 2 [1] [1] 2 amtB ammonium transporter
* * ÷ NC_000913 493306 493371 66 2 [1] [1] 2 dnaX
dnaX		 DNA polymerase III subunit tau
DNA polymerase III subunit tau
* * ÷ NC_000913 493463 493540 78 2 [1] [1] 2 dnaX DNA polymerase III subunit tau
* * ÷ NC_000913 494498 494576 79 3 [0] [1] 2 recR recombination mediator protein RecR
* * ÷ NC_000913 523389 523524 136 2 [1] [1] 2 rhsD protein RhsD
* * ÷ NC_000913 523700 523774 75 2 [1] [1] 2 rhsD protein RhsD
* * ÷ NC_000913 523864 524118 255 2 [1] [1] 3 rhsD protein RhsD
* * ÷ NC_000913 524284 524499 216 2 [1] [1] 2 rhsD protein RhsD
* * ÷ NC_000913 525667 525682 16 2 [1] [1] 2 rhsD protein RhsD
* * ÷ NC_000913 542334 542414 81 2 [1] [1] 2 glxK glycerate 2‑kinase 2
* * ÷ NC_000913 552814 552835 22 2 [1] [1] 2 purE N(5)‑carboxyaminoimidazole ribonucleotide mutase
* * ÷ NC_000913 598356 598372 17 2 [0] [1] 2 cusB copper/silver export system membrane fusion protein
* * ÷ NC_000913 621731 621757 27 2 [1] [0] 2 fepD ferric enterobactin ABC transporter membrane subunit FebD
* * ÷ NC_000913 621889 622014 126 2 [1] [1] 3 fepD ferric enterobactin ABC transporter membrane subunit FebD
* * ÷ NC_000913 633091 633192 102 2 [0] [1] 2 hcxA hydroxycarboxylate dehydrogenase A
* * ÷ NC_000913 723577 723721 145 3 [1] [1] 2 kdpD sensor histidine kinase KdpD
* * ÷ NC_000913 729663 729741 79 2 [1] [1] 2 rhsC rhs element protein RhsC
* * ÷ NC_000913 730029–730142 730499–730325 184–471 2 [1] [1] 2 rhsC rhs element protein RhsC
* * ÷ NC_000913 734716 734816 101 2 [1] [0] 3 ybfB/ybfC uncharacterized protein YbfB/uncharacterized protein YbfC
* * ÷ NC_000913 832065 832182 118 2 [1] [1] 2 rhlE ATP‑dependent RNA helicase RhlE
* * ÷ NC_000913 915147 915256 110 2 [1] [1] 2 lysO/aqpZ L‑lysine/thialysine exporter/water channel AqpZ
* * ÷ NC_000913 935511 935566 56 2 [1] [1] 2 ftsK cell division DNA translocase FtsK
* * ÷ NC_000913 1032620 1032636 17 2 [1] [1] 2 hyaA hydrogenase 1 small subunit
* * ÷ NC_000913 1080892 1080921 30 2 [1] [1] 2 putP/efeO proline:Na(+) symporter/ferrous iron transport system protein EfeO
* * ÷ NC_000913 1155088 1155100 13 2 [0] [1] 5 mltG endolytic murein transglycosylase
* * ÷ NC_000913 1191987 1192102 116 2 [1] [1] 2 [hflD] [hflD]
* * ÷ NC_000913 1294983 1295076 94 2 [0] [1] 3 tdk/adhE thymidine/deoxyuridine kinase/fused acetaldehyde‑CoA dehydrogenase and iron‑dependent alcohol dehydrogenasealdehyde/alcohol dehydrogenase AdhE
* * ÷ NC_000913 1363152 1363216 65 2 [1] [1] 2 puuC gamma‑glutamyl‑gamma‑aminobutyraldehyde dehydrogenase
* * ÷ NC_000913 1366422 1366492 71 2 [1] [1] 2 puuE 4‑aminobutyrate aminotransferase PuuE
* * ÷ NC_000913 1379007 1379023 17 2 [1] [0] 2 ycjT kojibiose phosphorylase
* * ÷ NC_000913 1429490 1429521 32 2 [1] [0] 2 stfR putative prophage side tail fiber protein StfR
* * ÷ NC_000913 1429957 1429974 18 3 [1] [1] 2 stfR putative prophage side tail fiber protein StfR
* * ÷ NC_000913 1430088 1430094 7 2 [1] [1] 2 stfR putative prophage side tail fiber protein StfR
* * ÷ NC_000913 1430282 1430323 42 2 [1] [1] 2 stfR putative prophage side tail fiber protein StfR
* * ÷ NC_000913 1438777 1438844 68 2 [1] [1] 2 ydbK putative pyruvate‑flavodoxin oxidoreductase
* * ÷ NC_000913 1461736 1461818 83 2 [1] [1] 4 paaJ beta‑ketoadipyl‑CoA thiolase
* * ÷ NC_000913 1528117 1528235 119 2 [1] [1] 2 yncH/ydcD DUF5445 domain‑containing protein YncH/uncharacterized protein YdcD
* * ÷ NC_000913 1698905 1699023 119 2 [1] [1] 2 malI DNA‑binding transcriptional repressor MalI
* * ÷ NC_000913 1769683 1769710 28 2 [1] [1] 2 ydiK putative transporter YdiK
* * ÷ NC_000913 2039621 2039639 19 2 [1] [1] 2 msrP protein‑L‑methionine sulfoxide reductase catalytic subunit MsrP
* * ÷ NC_000913 2057814 2057825 12 2 [1] [1] 2 yeeN/asnW putative transcriptional regulator YeeN/tRNA‑Asn
* * ÷ NC_000913 2154172 2154287 116 2 [1] [1] 2 mdtA multidrug efflux pump membrane fusion protein MdtA
* * ÷ NC_000913 2155793 2155863 71 2 [1] [0] 2 mdtB multidrug efflux pump RND permease subunit MdtB
* * ÷ NC_000913 2161254 2161342 89 2 [1] [1] 2 mdtC multidrug efflux pump RND permease subunit MdtC
* * ÷ NC_000913 2181984 2182042 59 2 [1] [1] 2 yegV putative sugar kinase YegV
* * ÷ NC_000913 2207592 2207635 44 2 [1] [1] 3 yehM uncharacterized protein YehM
* * ÷ NC_000913 2229197 2229212 16 2 [1] [1] 2 yohP/dusC putative membrane protein YohP/tRNA‑dihydrouridine(16) synthase
* * ÷ NC_000913 2252994 2253035 42 2 [1] [0] 2 nupX putative nucleoside transporter
* * ÷ NC_000913 2279465 2279524 60 2 [1] [1] 2 bcr multidrug efflux pump Bcr
* * ÷ NC_000913 2300127 2300165 39 2 [0] [1] 2 napG ferredoxin‑type protein NapG
* * ÷ NC_000913 2302644 2302681 38 2 [1] [1] 2 napA periplasmic nitrate reductase subunit NapA
* * ÷ NC_000913 2352710 2352794 85 2 [0] [1] 2 glpA anaerobic glycerol‑3‑phosphate dehydrogenase subunit A
* * ÷ NC_000913 2377929 2378090 162 2 [1] [1] 2 menD 2‑succinyl‑5‑enolpyruvyl‑6‑hydroxy‑3‑ cyclohexene‑1‑carboxylate synthase
* * ÷ NC_000913 2431414 2431508 95 2 [1] [1] 2 dedD cell division protein DedD
* * ÷ NC_000913 2441228 2441266 39 2 [1] [1] 2 fabB 3‑oxoacyl‑[acyl carrier protein] synthase 1
* * ÷ NC_000913 2530748 2530923 176 2 [1] [1] 2 zipA cell division protein ZipA
* * ÷ NC_000913 2540352 2540413 62 3 [1] [1] 2 cysA sulfate/thiosulfate ABC transporter ATP binding subunit
* * ÷ NC_000913 2547729 2547745 17 4 [0] [1] 2 murP N‑acetylmuramic acid‑specific PTS enzyme IICB component/anhydro‑N‑acetylmuramic acid transporter
* * ÷ NC_000913 2565921 2566017 97 2 [1] [1] 4 eutA ethanolamine ammonia‑lyase reactivase EutA
* * ÷ NC_000913 2566206 2566295 90 3 [1] [1] 2 eutA ethanolamine ammonia‑lyase reactivase EutA
* * ÷ NC_000913 2570207 2570213 7 2 [1] [1] 2 eutJ putative ethanolamine utilization chaperonin EutJ
* * ÷ NC_000913 2572911 2572992 82 2 [1] [1] 2 eutD phosphate acetyltransferase EutD
* * ÷ NC_000913 2573754 2573854 101 2 [1] [1] 2 eutT putative ethanolamine utilization cobalamin adenosyltransferase
* * ÷ NC_000913 2655281 2655342 62 2 [1] [1] 2 pepB aminopeptidase B
* * ÷ NC_000913 2658496 2658543 48 2 [1] [1] 2 hscA iron‑sulfur cluster biosynthesis chaperone HscA
* * ÷ NC_000913 2693406 2693492 87 2 [1] [1] 2 purL phosphoribosylformylglycinamide synthetase
* * ÷ NC_000913 2694544 2694593 50 2 [1] [1] 3 purL phosphoribosylformylglycinamide synthetase
* * ÷ NC_000913 2791408 2791500 93 2 [0] [1] 3 gabD succinate‑semialdehyde dehydrogenase (NADP(+)) GabD
* * ÷ NC_000913 2791798 2792006 209 3 [1] [1] 3 gabD succinate‑semialdehyde dehydrogenase (NADP(+)) GabD
* * ÷ NC_000913 2793460 2793594 135 2 [1] [0] 2 gabT 4‑aminobutyrate aminotransferase GabT
* * ÷ NC_000913 2836642 2836670 29 2 [1] [1] 2 hypF carbamoyl‑‑[HypE] ligase
* * ÷ NC_000913 2847335 2847351 17 2 [1] [1] 3 hycD formate hydrogenlyase subunit HycD
* * ÷ NC_000913 2954338 2954348 11 3 [1] [1] 2 recB exodeoxyribonuclease V subunit RecB
* * ÷ NC_000913 3046628 3046638 11 2 [1] [0] 5 gcvP glycine decarboxylase
* * ÷ NC_000913 3126176 3126235 60 2 [1] [1] 2 glcE glycolate dehydrogenase, putative FAD‑binding subunit
* * ÷ NC_000913 3272917 3272955 39 2 [1] [1] 2 garL alpha‑dehydro‑beta‑deoxy‑D‑glucarate aldolase
* * ÷ NC_000913 3297755 3297772 18 3 [1] [0] 2 yraQ permease family protein YraQ
* * ÷ NC_000913 3423883–3424233 3424461–3424240 8–579 2 [1] [1] 2 rrlD 23S ribosomal RNA
* * ÷ NC_000913 3505739 3505825 87 2 [1] [1] 2 yhfS putative aminotransferase YhfS
* * ÷ NC_000913 3538171 3538253 83 3 [1] [0] 2 yhgF putative RNA‑binding protein YhgF
* * ÷ NC_000913 3539596 3539668 73 2 [1] [1] 2 yhgF putative RNA‑binding protein YhgF
* * ÷ NC_000913 3556486 3556714 229 2 [1] [1] 2 rtcA RNA 3'‑terminal phosphate cyclase
* * ÷ NC_000913 3588762 3588770 9 2 [1] [1] 2 ugpC sn‑glycerol 3‑phosphate ABC transporter ATP binding subunit
* * ÷ NC_000913 3615815 3615869 55 3 [1] [1] 2 nikB Ni(2(+)) ABC transporter membrane subunit NikB
* * ÷ NC_000913 3616261 3616277 17 2 [0] [1] 2 nikC Ni(2(+)) ABC transporter membrane subunit NikC
* * ÷ NC_000913 3617159 3617164 6 2 [1] [0] 2 nikD Ni(2(+)) ABC transporter ATP binding subunit NikD
* * ÷ NC_000913 3619296 3620964–3619934 639–1669 3 [1] [1] 2 rhsB rhs element protein RhsB
* * ÷ NC_000913 3622425 3622554–3622442 18–130 2 [1] [0] 3 rhsB rhs element protein RhsB
* * ÷ NC_000913 3702011 3702070 60 2 [1] [1] 2 dppF dipeptide ABC transporter ATP binding subunit DppF
* * ÷ NC_000913 3704364 3704573 210 2 [1] [1] 2 dppC dipeptide ABC transporter membrane subunit DppC
* * ÷ NC_000913 3747159 3747200 42 2 [1] [1] 3 lyxK L‑xylulose kinase
* * ÷ NC_000913 3762258 3763876–3762925 668–1619 2 [1] [1] 2 rhsA rhs element protein RhsA
* * ÷ NC_000913 3765410 3765519–3765433 24–110 4 [1] [1] 2 rhsA rhs element protein RhsA
* * ÷ NC_000913 3851531 3851532 2 2 [0] [0] 2 ilvB acetohydroxy acid synthase I subunit IlvB
* * ÷ NC_000913 3854867 3854986 120 2 [1] [1] 2 emrD multidrug efflux pump EmrD
* * ÷ NC_000913 3855255 3855274 20 2 [1] [1] 2 yidF uncharacterized protein YidF
* * ÷ NC_000913 3873265 3873276 12 3 [1] [1] 3 dgoA 2‑dehydro‑3‑deoxy‑6‑phosphogalactonate aldolase
* * ÷ NC_000913 3878877 3878991 115 2 [1] [1] 2 gyrB DNA gyrase subunit B
* * ÷ NC_000913 3883427 3883442 16 2 [1] [1] 2 dnaA chromosomal replication initiator protein DnaA
* * ÷ NC_000913 3955710 3955849 140 2 [1] [1] 3 ilvA threonine deaminase
* * ÷ NC_000913 3995929 3995951 23 2 [0] [1] 2 yigA DUF484 domain‑containing protein YigA
* * ÷ NC_000913 4006361 4006434 74 2 [1] [1] 2 recQ ATP‑dependent DNA helicase RecQ
* * ÷ NC_000913 4125265 4125392 128 5 [1] [1] 2 priA primosomal protein N'
* * ÷ NC_000913 4199319 4199362 44 2 [1] [1] 2 nfi endonuclease V
* * ÷ NC_000913 4274526 4274597 72 2 [0] [1] 2 ssb ssDNA‑binding protein
* * ÷ NC_000913 4299705 4299767 63 2 [1] [1] 2 mdtP putative multidrug efflux pump outer membrane channel
* * ÷ NC_000913 4314968 4315058 91 2 [1] [1] 2 phnP 5‑phospho‑alpha‑D‑ribosyl 1,2‑cyclic phosphate phosphodiesterase
* * ÷ NC_000913 4315743 4315812 70 2 [1] [1] 2 phnN ribose 1,5‑bisphosphate phosphokinase
* * ÷ NC_000913 4316485 4316499 15 2 [1] [1] 2 phnM RPnTP hydrolase
* * ÷ NC_000913 4316554 4316572 19 2 [1] [0] 3 phnM RPnTP hydrolase
* * ÷ NC_000913 4316969 4317022 54 2 [1] [1] 2 phnM RPnTP hydrolase
* * ÷ NC_000913 4317455 4317507 53 2 [1] [1] 2 phnL methylphosphonate degradation complex subunit PhnL
* * ÷ NC_000913 4318213 4318229 17 3 [1] [1] 4 phnK carbon‑phosphorus lyase subunit PhnK
* * ÷ NC_000913 4318414 4318462 49 2 [1] [1] 2 phnK carbon‑phosphorus lyase subunit PhnK
* * ÷ NC_000913 4319774 4319833 60 2 [1] [0] 2 phnI carbon‑phosphorus lyase core complex subunit PhnI
* * ÷ NC_000913 4320143 4320202 60 2 [1] [1] 2 phnI carbon‑phosphorus lyase core complex subunit PhnI
* * ÷ NC_000913 4320411 4320510 100 2 [1] [0] 2 phnI carbon‑phosphorus lyase core complex subunit PhnI
* * ÷ NC_000913 4321448 4321592 145 2 [1] [1] 2 phnG carbon‑phosphorus lyase core complex subunit PhnG
* * ÷ NC_000913 4321837 4321948 112 2 [0] [1] 2 phnF putative transcriptional regulator PhnF
* * ÷ NC_000913 4322744 4322975 232 2 [1] [1] 2 phnF/phnD putative transcriptional regulator PhnF/phosphonate/phosphate ABC transporter periplasmic binding protein
* * ÷ NC_000913 4396505 4396532 28 2 [1] [1] 2 amiB N‑acetylmuramoyl‑L‑alanine amidase B
* * ÷ NC_000913 4503046 4503093 48 2 [1] [1] 2 insG IS4 family putative transposase
* * ÷ NC_000913 4512040 4512048 9 3 [1] [1] 2 fecD ferric citrate ABC transporter membrane subunit FecD
* * ÷ NC_000913 4512433 4512474 42 2 [1] [1] 2 fecC ferric citrate ABC transporter membrane subunit FecC
* * ÷ NC_000913 4515783 4515795 13 2 [1] [0] 4 fecA ferric citrate outer membrane transporter
* * ÷ NC_000913 4515979 4516201 223 3 [1] [1] 2 fecA ferric citrate outer membrane transporter

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =21 (1.080)8 (0.450) 8/352 NT 37.0% coding (290/630 nt) ycfK protein StfP
?NC_000913 1209619 = 8 (0.450)intergenic (‑500/‑66) tfaE/pinE putative tail fiber assembly protein TfaE/site‑specific DNA recombinase