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]
JC JC 622,244 IS5 (–) +4 bp 100% intergenic (‑55/‑53) fepD ← / → entS ferric enterobactin ABC transporter membrane subunit FebD/enterobactin exporter EntS
MC JC 1,299,499 Δ1,199 bp 100% insH21 insH21
MC JC 1,978,503 Δ776 bp 100% insB‑5–insA‑5 insB‑5, insA‑5
JC JC 1,979,486 IS5 (+) +4 bp 100% intergenic (‑271/‑264) insA‑5 ← / → uspC IS1 protein InsA/universal stress protein C
RA 2,173,361 Δ2 bp 100% pseudogene (917‑918/1358 nt) gatC ← galactitol‑specific PTS enzyme IIC component
JC JC 2,866,695 IS1 (+) +9 bp 50.0% coding (849‑857/993 nt) rpoS ← RNA polymerase, sigma S (sigma 38) factor
RA 3,560,455:1 +G 100% pseudogene (151/758 nt) glpR ← DNA‑binding transcriptional repressor GlpR
RA 4,296,060 C→T 23.5% 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 4,514,119 C→T 55.6% D64N (GAT→AAT)  fecB ← ferric citrate ABC transporter periplasmic binding protein
RA 4,515,480 C→T 100% G400S (GGC→AGC)  fecA ← ferric citrate outer membrane transporter

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 93730 93739 10 4 [0] [0] 2 murE UDP‑N‑acetylmuramoyl‑L‑alanyl‑D‑glutamate‑‑2, 6‑diaminopimelate ligase
* * ÷ NC_000913 164571 164612 42 2 [1] [1] 2 hrpB/mrcB putative ATP‑dependent RNA helicase HrpB/peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcB
* * ÷ NC_000913 218285 218296 12 2 [1] [1] 2 proS proline‑‑tRNA ligase
* * ÷ NC_000913 283855 283955 101 2 [0] [1] 2 yagF CP4‑6 prophage; D‑xylonate dehydratase
* * ÷ NC_000913 287544 287656 113 2 [1] [1] 2 yagH CP4‑6 prophage; putative xylosidase/arabinosidase
* * ÷ NC_000913 300093 300120 28 2 [1] [1] 2 paoC aldehyde dehydrogenase: molybdenum cofactor‑binding subunit
* * ÷ NC_000913 369840 369852 13 2 [1] [1] 3 mhpA putative 3‑(3‑hydroxyphenyl)propanoate/3‑hydroxycinnamate hydroxylase
* * ÷ NC_000913 375170 375202 33 2 [1] [1] 3 mhpE/mhpT 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter
* * ÷ NC_000913 401324 401328 5 2 [0] [0] 2 ddlA/iraP D‑alanine‑‑D‑alanine ligase A/anti‑adaptor protein for sigma(S) stabilization
* * ÷ NC_000913 445222 445228 7 2 [1] [0] 3 yajQ/yajR nucleotide binding protein/putative major facilitator superfamily transport protein YajR
* * ÷ NC_000913 448770 448776 7 2 [1] [0] 3 cyoB cytochrome bo3 ubiquinol oxidase subunit 1
* * ÷ NC_000913 486641 486696 56 2 [1] [1] 2 mscK potassium dependent, small conductance mechanosensitive channel
* * ÷ NC_000913 510242 510259 18 2 [1] [1] 2 copA Cu(+) exporting P‑type ATPase
* * ÷ NC_000913 598702 598718 17 2 [1] [1] 2 [cusB]–[cusA] [cusB],[cusA]
* * ÷ NC_000913 599196 599202 7 2 [1] [1] 2 cusA copper/silver export system RND permease
* * ÷ NC_000913 599830 599865 36 2 [1] [1] 2 cusA copper/silver export system RND permease
* * ÷ NC_000913 600289 600318 30 2 [1] [0] 2 cusA copper/silver export system RND permease
* * ÷ NC_000913 602485 602497 13 2 [0] [1] 2 pheP phenylalanine:H(+) symporter PheP
* * ÷ NC_000913 605311 605363 53 2 [1] [1] 2 nfsB NAD(P)H nitroreductase NfsB
* * ÷ NC_000913 610324 610391 68 2 [1] [1] 2 fepA ferric enterobactin outer membrane transporter
* * ÷ NC_000913 610453 610468 16 2 [1] [1] 2 fepA ferric enterobactin outer membrane transporter
* * ÷ NC_000913 612063 612120 58 2 [1] [1] 2 fepA ferric enterobactin outer membrane transporter
* * ÷ NC_000913 618665 618730 66 2 [1] [1] 2 fepE polysaccharide co‑polymerase family protein FepE
* * ÷ NC_000913 628836 628889 54 2 [0] [1] 2 entA 2,3‑dihydro‑2,3‑dihydroxybenzoate dehydrogenase
* * ÷ NC_000913 629530 629547 18 2 [0] [1] 2 entH proofreading thioesterase in enterobactin biosynthesis
* * ÷ NC_000913 632053 632073 21 2 [1] [1] 2 cstA/ybdD carbon starvation protein A/conserved protein YbdD
* * ÷ NC_000913 729294 729314 21 2 [1] [1] 2 ybfA DUF2517 domain‑containing protein YbfA
* * ÷ NC_000913 751341 751351 11 2 [1] [1] 2 ybgQ putative fimbrial usher protein YbgQ
* * ÷ NC_000913 791627 791681 55 2 [1] [0] 3 galE UDP‑glucose 4‑epimerase
* * ÷ NC_000913 798169 798202 34 2 [1] [1] 2 ybhA pyridoxal phosphate/fructose‑1,6‑bisphosphate phosphatase
* * ÷ NC_000913 841842 841917 76 2 [1] [1] 2 mcbA DUF1471 domain‑containing protein McbA
* * ÷ NC_000913 882268 882306 39 2 [1] [1] 2 deoR DNA‑binding transcriptional repressor DeoR
* * ÷ NC_000913 905250 905286 37 2 [1] [1] 2 amiD N‑acetylmuramoyl‑L‑alanine amidase D
* * ÷ NC_000913 938554 938568 15 2 [0] [0] 2 rarA recombination factor
* * ÷ NC_000913 952909 952946 38 2 [1] [1] 2 pflB pyruvate formate‑lyase
* * ÷ NC_000913 994889 994898 10 2 [1] [1] 2 ssuD FMNH2‑dependent alkanesulfonate monooxygenase
* * ÷ NC_000913 1039581 1039588 8 2 [1] [0] 2 appB cytochrome bd‑II ubiquinol oxidase subunit II
* * ÷ NC_000913 1079544 1079580 37 2 [1] [1] 3 putP proline:Na(+) symporter
* * ÷ NC_000913 1096033 1096042 10 2 [1] [0] 2 ycdU uncharacterized protein YcdU
* * ÷ NC_000913 1102375 1102411 37 2 [1] [1] 2 csgE curli transport specificity factor
* * ÷ NC_000913 1129313 1129344 32 2 [1] [1] 2 murJ putative lipid II flippase MurJ
* * ÷ NC_000913 1197628 1197640 13 3 [1] [0] 3 ymfE e14 prophage; uncharacterized protein YmfE
* * ÷ NC_000913 1200727 1200740 14 2 [1] [1] 2 intE e14 prophage; putative integrase
* * ÷ NC_000913 1208894 1208927 34 2 [1] [1] 2 tfaE e14 prophage; putative tail fiber assembly protein TfaE
* * ÷ NC_000913 1210735 1210747 13 2 [1] [1] 2 mcrA e14 prophage; 5‑methylcytosine‑specific restriction enzyme McrA
* * ÷ NC_000913 1258981 1259070 90 2 [1] [1] 2 [ychH] [ychH]
* * ÷ NC_000913 1282279 1282289 11 2 [1] [1] 2 narG nitrate reductase A subunit alpha
* * ÷ NC_000913 1329478 1329484 7 5 [0] [1] 2 sohB S49 peptidase family protein
* * ÷ NC_000913 1430317 1430347 31 2 [1] [1] 2 stfR Rac prophage; putative membrane protein
* * ÷ NC_000913 1443710 1443720 11 2 [1] [1] 2 ydbH PF11739 family protein YdbH
* * ÷ NC_000913 1479823 1479833 11 2 [1] [1] 2 ynbC hydrolase/methyltransferase domain‑containing protein YnbC
* * ÷ NC_000913 1510365 1510372 8 2 [1] [1] 2 ydcR fused putative DNA‑binding transcriptional regulator/putative aminotransferase YdcR
* * ÷ NC_000913 1528039 1528069 31 2 [1] [1] 2 rhsE RhsE protein in rhs element
* * ÷ NC_000913 1542996 1542999 4 2 [1] [0] 2 narU nitrate/nitrite transporter NarU
* * ÷ NC_000913 1555029 1555035 7 2 [1] [0] 3 maeA malate dehydrogenase, NAD‑requiring
* * ÷ NC_000913 1563512 1563529 18 2 [1] [1] 2 dosP oxygen‑sensing c‑di‑GMP phosphodiesterase DosP
* * ÷ NC_000913 1580138 1580155 18 2 [0] [1] 2 ydeM putative anaerobic sulfatase maturation enzyme YdeM
* * ÷ NC_000913 1603602 1603606 5 4 [0] [1] 2 lsrC Autoinducer‑2 ABC transporter membrane subunit LsrC
* * ÷ NC_000913 1606167 1606186 20 2 [1] [1] 2 lsrF 3‑hydroxy‑2,4‑pentadione 5‑phosphate thiolase
* * ÷ NC_000913 1611376 1611434 59 2 [1] [1] 2 dgcF putative diguanylate cyclase DgcF
* * ÷ NC_000913 1622556 1622586 31 2 [1] [1] 2 ydeE/mgtS dipeptide exporter/small protein MgtS
* * ÷ NC_000913 1628439 1628519 81 2 [1] [1] 2 ydfH DNA‑binding transcriptional repressor YdfH
* * ÷ NC_000913 1656537 1656636 100 2 [1] [1] 2 speG spermidine N‑acetyltransferase
* * ÷ NC_000913 1674754 1674830 77 2 [1] [1] 2 tqsA autoinducer 2 exporter
* * ÷ NC_000913 1734463 1734512 50 2 [1] [0] 2 mepH peptidoglycan DD‑endopeptidase MepH
* * ÷ NC_000913 1787261 1787288 28 2 [1] [1] 2 ppsA/ppsR phosphoenolpyruvate synthetase/posphoenolpyruvate synthetase regulatory protein
* * ÷ NC_000913 1802967 1802975 9 2 [1] [1] 2 thrS/arpB threonine‑‑tRNA ligase/putative ankyrin repeat protein B, N‑terminal fragment
* * ÷ NC_000913 1823093 1823111 19 2 [1] [1] 2 nadE NAD synthetase, NH3‑dependent
* * ÷ NC_000913 1849961 1850018 58 2 [1] [1] 2 sppA protease IV, a signal peptide peptidase
* * ÷ NC_000913 1856107 1856130 24 2 [1] [1] 2 ydjH putative sugar kinase YdjH
* * ÷ NC_000913 1858146 1858166 21 2 [1] [1] 2 ydjJ putative zinc‑binding dehydrogenase YdjJ
* * ÷ NC_000913 1902355 1902378 24 2 [1] [1] 2 manX mannose‑specific PTS enzyme IIAB component
* * ÷ NC_000913 1957963 1958017 55 2 [1] [1] 3 torY cytochrome c quinol dehydrogenase TorY
* * ÷ NC_000913 1964062 1964080 19 2 [1] [1] 2 flhA flagellar biosynthesis protein FlhA
* * ÷ NC_000913 1969714 1969735 22 4 [0] [1] 2 tap methyl‑accepting chemotaxis protein Tap
* * ÷ NC_000913 1976183 1976200 18 2 [1] [1] 2 motB motility protein B
* * ÷ NC_000913 1991639 1991683 45 2 [1] [1] 2 yecA/leuZ UPF0149 family protein YecA/tRNA‑Leu
* * ÷ NC_000913 1993827 1993842 16 2 [1] [1] 2 uvrC excision nuclease subunit C
* * ÷ NC_000913 1993903 1993920 18 2 [1] [1] 2 uvrC excision nuclease subunit C
* * ÷ NC_000913 2030262 2030270 9 2 [1] [1] 2 yedA putative transporter YedA
* * ÷ NC_000913 2044885 2044902 18 2 [1] [0] 3 asnT/yeeJ tRNA‑Asn/inverse autotransporter adhesin
* * ÷ NC_000913 2106123 2106201 79 2 [1] [1] 2 wbbH putative O‑antigen polymerase
* * ÷ NC_000913 2116330 2116352 23 2 [1] [0] 2 wcaL putative colanic biosynthesis glycosyl transferase
* * ÷ NC_000913 2159839 2159848 10 2 [1] [1] 3 mdtC multidrug efflux pump RND permease subunit MdtC
* * ÷ NC_000913 2163325 2163331 7 2 [1] [1] 2 baeS sensory histidine kinase BaeS
* * ÷ NC_000913 2426398 2426423 26 3 [1] [1] 2 hisJ histidine ABC transporter periplasmic binding protein
* * ÷ NC_000913 2442510 2442524 15 3 [0] [1] 2 mnmC fused 5‑methylaminomethyl‑2‑thiouridine‑forming methyltransferase and FAD‑dependent demodification enzyme
* * ÷ NC_000913 2448820 2448828 9 2 [1] [1] 2 smrB putative endonuclease SmrB
* * ÷ NC_000913 2487868 2487880 13 2 [0] [1] 2 evgS sensory histidine kinase EvgS
* * ÷ NC_000913 2498240 2498299 60 2 [1] [1] 2 [alaC] [alaC]
* * ÷ NC_000913 2518881 2518894 14 2 [1] [1] 2 yfeD putative DNA‑binding transcriptional regulator YfeD
* * ÷ NC_000913 2546167 2546177 11 2 [0] [1] 2 murQ N‑acetylmuramic acid 6‑phosphate etherase
* * ÷ NC_000913 2611635 2611652 18 2 [1] [0] 3 hyfJ putative hydrogenase 4 assembly protein
* * ÷ NC_000913 2644897 2644904 8 2 [1] [1] 2 ndk/pbpC nucleoside diphosphate kinase/peptidoglycan glycosyltransferase PbpC
* * ÷ NC_000913 2650227 2650252 26 2 [1] [0] 2 yfhM alpha2‑macroglobulin
* * ÷ NC_000913 2675387 2675401 15 2 [1] [1] 2 yphC putative zinc‑binding dehydrogenase YphC
* * ÷ NC_000913 2689061 2689065 5 2 [1] [1] 3 qseG outer membrane lipoprotein QseG
* * ÷ NC_000913 2780243 2780263 21 2 [1] [1] 2 ypjA adhesin‑like autotransporter YpjA
* * ÷ NC_000913 2780360 2780375 16 2 [0] [1] 2 ypjA adhesin‑like autotransporter YpjA
* * ÷ NC_000913 2802265 2802285 21 2 [1] [1] 2 nrdE ribonucleoside‑diphosphate reductase 2 subunit alpha
* * ÷ NC_000913 2834574 2834646 73 2 [1] [0] 2 norW NADH:flavorubredoxin reductase
* * ÷ NC_000913 2906441 2906461 21 2 [1] [1] 2 ygcG protein YgcG
* * ÷ NC_000913 3017841 3017880 40 2 [1] [1] 2 ygfK putative oxidoreductase, Fe‑S subunit
* * ÷ NC_000913 3030888 3030895 8 2 [0] [1] 2 ygfT fused putative oxidoreductase, Fe‑S subunit and nucleotide‑binding subunit
* * ÷ NC_000913 3069790 3069842 53 2 [1] [1] 2 [mscS] [mscS]
* * ÷ NC_000913 3158264 3158279 16 2 [1] [1] 2 yqhG DUF3828 domain‑containing protein YqhG
* * ÷ NC_000913 3168523 3168530 8 2 [1] [0] 2 mqsR mRNA interferase/toxin of the MqsR‑MqsA toxin‑antitoxin system
* * ÷ NC_000913 3197262 3197274 13 2 [0] [1] 2 glnE fused glutamine synthetase deadenylase/glutamine synthetase adenylyltransferase
* * ÷ NC_000913 3227823 3227828 6 2 [0] [1] 2 ygjJ protein YgjJ
* * ÷ NC_000913 3279165 3279188 24 2 [1] [1] 2 kbaZ tagatose‑1,6‑bisphosphate aldolase 1 subunit KbaZ
* * ÷ NC_000913 3305648 3305658 11 2 [1] [1] 2 mtr tryptophan:H(+) symporter Mtr
* * ÷ NC_000913 3324414 3324440 27 2 [1] [1] 2 folP dihydropteroate synthase
* * ÷ NC_000913 3423814–3424234 3424541–3424243 10–728 2 [1] [1] 2 [rrlD] [rrlD]
* * ÷ NC_000913 3496914 3496928 15 4 [0] [0] 2 nirD/nirC nitrite reductase subunit NirD/nitrite transporter NirC
* * ÷ NC_000913 3588727 3588754 28 2 [1] [0] 2 ugpC sn‑glycerol 3‑phosphate ABC transporter ATP binding subunit
* * ÷ NC_000913 3635845 3635849 5 5 [1] [0] 2 yhiM inner membrane protein with a role in acid resistance
* * ÷ NC_000913 3714987 3715030 44 2 [1] [0] 3 bisC biotin sulfoxide reductase
* * ÷ NC_000913 3748459 3748483 25 2 [1] [1] 2 lyxK L‑xylulose kinase
* * ÷ NC_000913 3781128 3781142 15 2 [0] [1] 3 lldD/trmL L‑lactate dehydrogenase/tRNA (cytidine/uridine‑2'‑O)‑ribose methyltransferase
* * ÷ NC_000913 3848315 3848327 13 3 [1] [0] 2 uhpC inner membrane protein sensing glucose‑6‑phosphate
* * ÷ NC_000913 3850758 3850774 17 2 [0] [0] 3 uhpA/ilvN DNA‑binding transcriptional activator UhpA/acetohydroxy acid synthase I subunit IlvN
* * ÷ NC_000913 3874683 3874691 9 2 [1] [1] 2 dgoR putative DNA‑binding transcriptional regulator DgoR
* * ÷ NC_000913 3886846 3886857 12 2 [1] [0] 2 mnmE 5‑carboxymethylaminomethyluridine‑tRNA synthase GTPase subunit
* * ÷ NC_000913 3954853 3954857 5 2 [1] [0] 3 ilvD dihydroxy‑acid dehydratase
* * ÷ NC_000913 4010370 4010375 6 2 [1] [1] 2 yigL phosphosugar phosphatase YigL
* * ÷ NC_000913 4073755 4073772 18 2 [1] [0] 2 yihV 6‑deoxy‑6‑sulfofructose kinase
* * ÷ NC_000913 4100154 4100211 58 2 [1] [1] 2 rhaT rhamnose/lyxose:H(+) symporter
* * ÷ NC_000913 4218942 4218959 18 2 [1] [1] 2 aceK isocitrate dehydrogenase kinase/phosphatase
* * ÷ NC_000913 4219038 4219049 12 2 [1] [1] 2 aceK isocitrate dehydrogenase kinase/phosphatase
* * ÷ NC_000913 4235970 4235979 10 2 [1] [1] 2 yjbE uncharacterized protein YjbE
* * ÷ NC_000913 4286308 4286314 7 2 [1] [1] 2 acs acetyl‑CoA synthetase (AMP‑forming)
* * ÷ NC_000913 4323889 4323895 7 2 [1] [0] 2 phnD phosphonate ABC transporter periplasmic binding protein
* * ÷ NC_000913 4375200 4375217 18 2 [1] [1] 2 epmB lysine 2,3‑aminomutase
* * ÷ NC_000913 4388629 4388651 23 2 [1] [1] 2 mscM miniconductance mechanosensitive channel MscM
* * ÷ NC_000913 4417258 4417288 31 2 [1] [1] 2 yjfP carboxylesterase
* * ÷ NC_000913 4445825 4445856 32 2 [1] [1] 2 tamB translocation and assembly module subunit TamB
* * ÷ NC_000913 4469112 4469158 47 2 [0] [1] 2 mgtA Mg(2(+)) importing P‑type ATPase
* * ÷ NC_000913 4537951 4537951 1 2 [0] [0] 2 nanM N‑acetylneuraminate mutarotase
* * ÷ NC_000913 4539355 4539414 60 2 [1] [1] 3 nanC N‑acetylneuraminic acid outer membrane channel
* * ÷ NC_000913 4542691 4542702 12 6 [0] [1] 2 fimE/fimA regulator for fimA/type 1 fimbriae major subunit
* * ÷ NC_000913 4615749 4615761 13 2 [1] [1] 2 yjjI DUF3029 domain‑containing protein YjjI

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 41643811 (0.820)4 (0.310) 4/250 NT 31.5% coding (515/1203 nt) sbcD ATP dependent, structure specific DNA nuclease ‑ SbcD subunit
?NC_000913 = 416786 7 (0.550)coding (167/1203 nt) sbcD ATP dependent, structure specific DNA nuclease ‑ SbcD subunit
* ? NC_000913 = 5982567 (0.520)7 (0.540) 6/256 NT 42.7% coding (778/1224 nt) cusB copper/silver export system membrane fusion protein
?NC_000913 636166 = 12 (0.920)coding (404/1221 nt) ybdN putative PAPS reductase/DUF3440 domain‑containing protein YbdN
* ? NC_000913 1207790 =6 (0.450)13 (1.100) 12/232 NT 71.7% coding (290/630 nt) ycfK e14 prophage; protein StfP
?NC_000913 1209619 = 5 (0.420)pseudogene (37/537 nt) stfE e14 prophage; putative side tail fiber protein fragment
* ? NC_000913 1941980 =8 (0.590)4 (0.320) 4/248 NT 29.1% coding (604/933 nt) znuA Zn(2(+)) ABC transporter periplasmic binding protein
?NC_000913 1942149 = 12 (0.950)coding (435/933 nt) znuA Zn(2(+)) ABC transporter periplasmic binding protein
* ? NC_000913 = 45426900 (0.000)4 (0.320) 4/246 NT 33.3% intergenic (+57/‑425) fimE/fimA regulator for fimA/type 1 fimbriae major subunit
?NC_000913 = 4542986 16 (1.270)intergenic (+353/‑129) fimE/fimA regulator for fimA/type 1 fimbriae major subunit