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

Predicted mutations
evidence position mutation annotation gene description
RA 188,837 C→T R316C (CGC→TGC)  PP_0165 → GGDEF domain‑containing protein
RA 233,545 C→T G548G (GGC→GGT)  PP_0180 → cytochrome c family protein
RA 476,133 A→T Q141L (CAG→CTG)  tsaD → tRNA N6‑adenosine(37)‑threonylcarbamoyltransferase complex transferase subunit TsaD
RA 545,874 C→G R1371G (CGT→GGT)  rpoC → DNA‑directed RNA polymerase subunit beta'
RA 548,171 G→C G340R (GGT→CGT)  fusA → elongation factor G 1
RA 1,011,323 +T intergenic (‑258/+192) PP_0871 ← / ← SBRG_Ecoli_galM glycine betaine/carnitine/choline ABC transporter permease/SBRG_Ecoli_galM
MC JC 1,515,811 (33-bp)2→1 pseudogene (715‑747/1851 nt) PP_1325 ← putative lipoprotein
RA 1,856,513 A→G D203G (GAT→GGT)  relA → ATP:GTP 3'‑pyrophosphotransferase
RA 4,018,201 G→A intergenic (+144/‑36) mvaB → / → PP_mr44 hydroxymethylglutaryl‑CoA lyase/CrcZ ncRNA
RA 4,163,464 A→C S161R (AGC→CGC)  PP_3661 → membrane protein
RA 4,746,222 +C intergenic (+464/+288) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,746,224 A→G intergenic (+466/+286) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,746,226 C→T intergenic (+468/+284) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,746,229 C→T intergenic (+471/+281) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,746,232 C→G intergenic (+474/+278) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,746,234 2 bp→CT intergenic (+476/+275) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,746,248 C→T intergenic (+490/+262) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,746,250 A→C intergenic (+492/+260) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,746,253 2 bp→GC intergenic (+495/+256) gltA → / ← yeiW citrate synthase/putative oxidoreductase

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_002947 85056 85191 136 2 [1] [1] 2 [PP_0075] [PP_0075]
* * ÷ NC_002947 97575 97611 37 2 [0] [1] 2 [PP_0091] [PP_0091]
* * ÷ NC_002947 170312 170328 17 2 [1] [0] 4 PP_0159 family III CoA‑transferase
* * ÷ NC_002947 170795 170865 71 2 [0] [1] 2 [PP_0159] [PP_0159]
* * ÷ NC_002947 171395–172965 176280–172979 15–4886 3 [1] [1] 2 [PP_16SA]–[PP_5SA] [PP_16SA],PP_23SA,[PP_5SA]
* * ÷ NC_002947 176674–178395 181708–178409 15–5035 2 [1] [1] 3 PP_16SB–[PP_r01] PP_16SB,PP_23SB,[PP_r01]
* * ÷ NC_002947 235335 235391 57 2 [1] [1] 3 PP_0183/argH glutathione S‑transferase/argininosuccinate lyase
* * ÷ NC_002947 284548 284630 83 3 [1] [1] 2 [betT‑II]–[atsK] [betT‑II],[atsK]
* * ÷ NC_002947 353090 353115 26 3 [0] [0] 2 hisF/cbcV imidazole glycerol phosphate synthase subunit HisF/choline/betaine/carnitine ABC transporter ATP binding protein
* * ÷ NC_002947 524148 524186 39 2 [0] [1] 2 tyrS/PP_16SC tyrosine‑‑tRNA ligase/16S ribosomal RNA
* * ÷ NC_002947 543569 543597 29 2 [1] [1] 2 rpoC DNA‑directed RNA polymerase subunit beta'
* * ÷ NC_002947 546488 546498 11 2 [1] [1] 3 rpsL 30S ribosomal protein S12
* * ÷ NC_002947 681290 681313 24 2 [0] [1] 2 PP_0583/PP_0584 AraC family transcriptional regulator/methyl‑accepting chemotaxis transducer
* * ÷ NC_002947 697082 697128 47 2 [1] [1] 2 mmsA‑I/PP_16SD methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA
* * ÷ NC_002947 796859 796888 30 2 [1] [1] 2 PP_0681/PP_0682 hypothetical protein/inner membrane protein
* * ÷ NC_002947 1003294 1003325 32 2 [1] [1] 2 speC/PP_0865 ornithine decarboxylase/ECF subfamily RNA polymerase sigma‑24 factor
* * ÷ NC_002947 1007427 1007555 129 2 [1] [1] 2 [PP_0867] [PP_0867]
* * ÷ NC_002947 1007887 1007910 24 3 [1] [1] 2 yehX ABC transporter ATP‑binding protein
* * ÷ NC_002947 1042751 1042817 67 2 [0] [1] 2 PP_0896/PP_0897 carbon‑nitrogen hydrolase family protein/class 1 fumarate hydratase
* * ÷ NC_002947 1118766 1118824 59 2 [1] [1] 2 [rlmF] [rlmF]
* * ÷ NC_002947 1161288 1161308 21 2 [1] [0] 2 PP_1013/yihS sensor histidine kinase/aldose‑ketose isomerase
* * ÷ NC_002947 1363713 1363781 69 2 [1] [1] 3 PP_1183 siderophore biosynthesis protein
* * ÷ NC_002947 1388207 1388218 12 2 [1] [1] 2 PP_1204 lipoprotein
* * ÷ NC_002947 1448076 1448111 36 2 [1] [0] 3 ghrB/PP_1262 2‑ketoaldonate reductase/hydroxypyruvate/glyoxylate reductase/LysR family transcriptional regulator
* * ÷ NC_002947 1469115 1469163 49 2 [1] [1] 3 [algL]–[algX] [algL],[algX]
* * ÷ NC_002947 1497189 1497203 15 3 [1] [1] 3 [cysNC] [cysNC]
* * ÷ NC_002947 1504381 1504476 96 3 [1] [1] 2 trpS/zapE tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein
* * ÷ NC_002947 1511850 1511961 112 2 [1] [1] 2 [sspA] [sspA]
* * ÷ NC_002947 1549467 1549485 19 3 [0] [0] 7 mdfA/ampG multidrug MFS transporter/muropeptide permease AmpG
* * ÷ NC_002947 1597568 1597635 68 3 [1] [1] 2 PP_1397 hypothetical protein
* * ÷ NC_002947 1644534 1644605 72 2 [1] [1] 2 czcR‑III/PP_1439 response regulator/hypothetical protein
* * ÷ NC_002947 1717045 1717112 68 2 [0] [1] 2 ppc/adk phosphoenolpyruvate carboxylase/adenylate kinase
* * ÷ NC_002947 1935397 1935445 49 2 [1] [1] 2 [apeB] [apeB]
* * ÷ NC_002947 1972174 1972193 20 3 [1] [0] 2 PP_1762/yciK hypothetical protein/putative oxidoreductase
* * ÷ NC_002947 2043203 2043412 210 2 [1] [1] 2 [rffE] [rffE]
* * ÷ NC_002947 2100203 2100226 24 2 [1] [1] 2 htpX/alaA protease HtpX/glutamate‑pyruvate aminotransferase
* * ÷ NC_002947 2104978 2105002 25 2 [0] [1] 3 PP_1875/PP_1876 two‑component system sensor histidine kinase/response regulator/AAA family ATP/GTP‑binding protein
* * ÷ NC_002947 2246253 2246333 81 4 [0] [1] 2 gltX/PP_t25 glutamate‑‑tRNA ligase/tRNA‑Ala
* * ÷ NC_002947 2300823 2300873 51 2 [1] [0] 2 PP_5496/PP_2023 hypothetical protein/glutathione S‑transferase family protein
* * ÷ NC_002947 2669026 2669046 21 2 [1] [1] 2 prpC/acnA‑II methylcitrate synthase/aconitate hydratase
* * ÷ NC_002947 2842075 2842114 40 2 [1] [1] 2 sad‑I/PP_2489 NAD+‑dependent succinate semialdehyde dehydrogenase/xenobiotic reductase
* * ÷ NC_002947 3058187 3058237 51 2 [1] [1] 2 [PP_2664]–[agmR] [PP_2664],[agmR]
* * ÷ NC_002947 3176754 3176776 23 2 [1] [0] 3 PP_2784 short‑chain dehydrogenase/reductase family oxidoreductase
* * ÷ NC_002947 3324146 3324183 38 2 [1] [1] 2 treSA/PP_2919 trehalose synthase A/LysR family transcriptional regulator
* * ÷ NC_002947 3781347 3781433 87 2 [1] [1] 2 PP_3338/PP_3339 cytochrome bd‑type quinol oxidase/hypothetical protein
* * ÷ NC_002947 4054903 4054915 13 2 [1] [0] 2 quiA/oprB‑III quinate dehydrogenase/carbohydrate‑selective porin
* * ÷ NC_002947 4155018 4155085 68 2 [0] [1] 2 PP_3654/PP_3655 leucine‑responsive regulatory protein/cytosine/purine/uracil/thiamine/allantoin permease family protein
* * ÷ NC_002947 4175121 4175209 89 2 [1] [1] 3 katG/PP_3669 catalase‑peroxidase/LysR family transcriptional regulator
* * ÷ NC_002947 4311593 4311635 43 3 [1] [1] 2 proC pyrroline‑5‑carboxylate reductase
* * ÷ NC_002947 4343478 4343503 26 2 [1] [1] 2 PP_3812/PP_5632 lipase/allo‑isoleucine metabolism protein
* * ÷ NC_002947 4345045 4345077 33 2 [1] [0] 2 ribAB‑II/PP_3814 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein
* * ÷ NC_002947 4358174 4358187 14 2 [1] [0] 2 yrpB 2‑nitropropane dioxygenase
* * ÷ NC_002947 4534983 4535046 64 2 [1] [1] 4 [PP_4018] [PP_4018]
* * ÷ NC_002947 4556970 4556989 20 2 [1] [0] 2 pydA/rutR NADP‑dependent dihydropyrimidine dehydrogenase subunit PreA/transcriptional regulator, TetR family
* * ÷ NC_002947 4680303 4680372 70 2 [1] [0] 2 PP_4137/chrR outer membrane siderophore receptor/chromate reductase
* * ÷ NC_002947 4692306 4692317 12 2 [1] [1] 2 PP_4148 ABC transporter permease
* * ÷ NC_002947 4745820 4745865 46 2 [1] [0] 2 gltA/yeiW citrate synthase/putative oxidoreductase
* * ÷ NC_002947 4801611 4801636 26 2 [1] [0] 2 pvdH/PP_4224 diaminobutyrate‑2‑oxoglutarate transaminase/sensor histidine kinase
* * ÷ NC_002947 4813174 4813202 29 66 [0] [0] 28 PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
* * ÷ NC_002947 4847877 4847895 19 2 [1] [1] 2 ccoP‑II/PP_4259 cbb3‑type cytochrome c oxidase subunit/iron‑sulfur cluster‑binding protein
* * ÷ NC_002947 4850156 4850192 37 2 [0] [1] 5 PP_4260/PP_4261 hypothetical protein/cation‑transporting P‑type ATPase
* * ÷ NC_002947 4955933 4955987 55 3 [1] [1] 3 fliL/fliK flagellar protein FliL/flagellar hook‑length control protein FliK
* * ÷ NC_002947 5073629 5073633 5 2 [0] [1] 2 PP_4465 porin
* * ÷ NC_002947 5102218 5102235 18 2 [0] [1] 2 PP_mr66/acsA‑I P6/acetyl‑CoA synthetase
* * ÷ NC_002947 5104944 5104992 49 2 [1] [0] 2 PP_4488/phhR hypothetical protein/sigma‑54 dependent transcriptional regulator
* * ÷ NC_002947 5178202 5178252 51 3 [1] [1] 2 fadD‑I/fadD‑II long‑chain‑fatty acid‑‑CoA ligase/long‑chain‑fatty acid‑‑CoA ligase
* * ÷ NC_002947 5197750 5197767 18 2 [1] [1] 2 PP_4572/PP_4573 hypothetical protein/AAA family ATPase
* * ÷ NC_002947 5204640 5204661 22 2 [0] [0] 2 PP_4579/PP_4580 LysR family transcriptional regulator/hypothetical protein
* * ÷ NC_002947 5215251 5215309 59 7 [0] [1] 2 [PP_4592] [PP_4592]
* * ÷ NC_002947 5261816 5261881 66 2 [1] [1] 2 [PP_5703] [PP_5703]
* * ÷ NC_002947 5279042 5279067 26 2 [0] [1] 2 rlmG/PP_4649 ribosomal RNA large subunit methyltransferase G/hypothetical protein
* * ÷ NC_002947 5397363 5397386 24 3 [0] [1] 2 PP_5710 hypothetical protein
* * ÷ NC_002947 5490063 5490187 125 2 [1] [1] 2 [purH] [purH]
* * ÷ NC_002947 5511550 5511583 34 2 [1] [0] 3 PP_4839/cycA iron‑regulated membrane protein/D‑alanine/beta‑alanine/D‑serine/glycine permease
* * ÷ NC_002947 5542044 5542052 9 2 [1] [0] 3 nadE/PP_4870 NH(3)‑dependent NAD(+) synthetase/azurin
* * ÷ NC_002947 5599092 5599186 95 4 [1] [0] 3 PP_4921/thiC NCS1 family transporter/phosphomethylpyrimidine synthase
* * ÷ NC_002947 5657972 5657989 18 2 [1] [1] 2 PP_4961/PP_4962 lipoprotein/hypothetical protein
* * ÷ NC_002947 5660627 5660639 13 3 [0] [1] 2 epd/tktA D‑erythrose 4‑phosphate dehydrogenase/transketolase A
* * ÷ NC_002947 5676596 5676705 110 2 [1] [0] 2 PP_4978/PP_4979 hypothetical protein/substrate‑binding protein
* * ÷ NC_002947 5756738 5756785 48 2 [1] [0] 4 thiI/glnA tRNA sulfurtransferase/glutamine synthetase
* * ÷ NC_002947 5779687 5779755 69 3 [1] [1] 3 betB NAD‑dependent betaine aldehyde dehydrogenase
* * ÷ NC_002947 5821902 5821905 4 3 [0] [0] 2 PP_5092/pilT NLP/P60 protein/twitching motility protein
* * ÷ NC_002947 5973486 5973499 14 2 [0] [1] 3 PP_5723 hypothetical protein
* * ÷ NC_002947 5989420 5989493 74 3 [1] [1] 4 PP_5242/ycaC‑II GAF domain‑containing sensor histidine kinase/putative hydrolase
* * ÷ NC_002947 6011580 6011586 7 4 [0] [0] 2 ydcJ/PP_5261 metalloprotein/LysR family transcriptional regulator
* * ÷ NC_002947 6014152 6014158 7 2 [0] [1] 6 norM/PP_5263 multidrug resistance protein NorM/GGDEF domain‑containing protein
* * ÷ NC_002947 6018847 6018862 16 17 [1] [1] 5 xpt/PP_5266 xanthine phosphoribosyltransferase/acetyl‑CoA hydrolase family protein
* * ÷ NC_002947 6082875 6082905 31 2 [1] [1] 2 PP_5329/PP_5330 phosphate ABC transporter substrate‑binding protein/MFS transporter
* * ÷ NC_002947 6094927 6094939 13 2 [0] [1] 3 [potF‑IV] [potF‑IV]
* * ÷ NC_002947 6131974 6131998 25 2 [1] [1] 2 [PP_5375] [PP_5375]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_002947 = 65278631 (1.280)26 (1.460) 9/194 0.5 69.5% coding (1960/1962 nt) ctpL methyl‑accepting chemotaxis protein CtpL
?NC_002947 4813203 = 0 (0.000)intergenic (‑318/‑237) PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
* ? NC_002947 1015841 =0 (0.000)21 (0.870) 15/264 0.3 100% intergenic (‑68/‑700) SBRG_Ecoli_galE/prfC SBRG_Ecoli_galE/peptide chain release factor 3
?NC_002947 4541196 = NA (NA)intergenic (+730/‑85) PP_4022/PP_4024 hypothetical protein/transposase
* ? NC_002947 = 10158481 (0.040)17 (0.700) 12/264 0.5 94.4% intergenic (‑75/‑693) SBRG_Ecoli_galE/prfC SBRG_Ecoli_galE/peptide chain release factor 3
?NC_002947 = 4543236 NA (NA)intergenic (+45/‑275) PP_4025/PP_4027 transposase/hypothetical protein
* ? NC_002947 1444956 =NA (NA)8 (0.340) 8/254 0.9 100% intergenic (‑331/‑328) yveA/PP_1260 aspartate‑proton symporter/transposase
?NC_002947 = 1849442 0 (0.000)coding (343/2754 nt) gacS sensor protein GacS
* ? NC_002947 1736154 =20 (0.830)4 (0.210) 3/208 1.5 23.7% intergenic (‑76/+115) dapE/PP_1526 succinyl‑diaminopimelate desuccinylase/beta‑(1‑3)‑glucosyl transferase
?NC_002947 1736246 = 10 (0.520)intergenic (‑168/+23) dapE/PP_1526 succinyl‑diaminopimelate desuccinylase/beta‑(1‑3)‑glucosyl transferase
* ? NC_002947 1849440 =0 (0.000)13 (0.550) 11/258 0.6 100% coding (345/2754 nt) gacS sensor protein GacS
?NC_002947 2942681 = NA (NA)intergenic (+46/+37) PP_2569/PP_2570 MHS family metabolite MFS transporter/transposase
* ? NC_002947 2477094 =2 (0.080)8 (0.470) 4/186 1.1 68.3% intergenic (+6/+143) PP_2166/PP_2167 anti‑anti‑sigma factor/PhoD‑like phosphatase
?NC_002947 2477218 = 6 (0.350)intergenic (+130/+19) PP_2166/PP_2167 anti‑anti‑sigma factor/PhoD‑like phosphatase
* ? NC_002947 = 24771322 (0.080)8 (0.470) 5/186 0.9 68.3% intergenic (+44/+105) PP_2166/PP_2167 anti‑anti‑sigma factor/PhoD‑like phosphatase
?NC_002947 = 2477178 6 (0.350)intergenic (+90/+59) PP_2166/PP_2167 anti‑anti‑sigma factor/PhoD‑like phosphatase
* ? NC_002947 3976787 =NA (NA)15 (0.720) 12/228 0.4 100% intergenic (+177/‑203) PP_3501/PP_3502 transposase/transposase
?NC_002947 4578248 = 0 (0.000)intergenic (+63/‑74) PP_4054/glgX hypothetical protein/glycogen debranching enzyme
* ? NC_002947 = 45782490 (0.000)32 (1.400) 23/250 0.1 100% intergenic (+64/‑73) PP_4054/glgX hypothetical protein/glycogen debranching enzyme
?NC_002947 = 5763126 NA (NA)intergenic (+145/+373) PP_5050/PP_5051 transposase/hypothetical protein
* ? NC_002947 = 48131730 (0.000)59 (2.680) 12/240 0.4 40.7% intergenic (‑288/‑267) PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
?NC_002947 5993770 = 172 (7.820)intergenic (+59/‑487) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA