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 451,198 C→T G226G (GGG→GGA)  PP_0371 ← LysR family transcriptional regulator
RA 476,133 A→T Q141L (CAG→CTG)  tsaD → tRNA N6‑adenosine(37)‑threonylcarbamoyltransferase complex transferase subunit TsaD
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 2,154,508 T→C D335G (GAC→GGC)  rne ← ribonuclease E
JC 3,582,655 (GCGCCTGT)1→2 coding (78/738 nt) PP_3158 → hypothetical protein
RA 4,018,201 G→A intergenic (+144/‑36) mvaB → / → PP_mr44 hydroxymethylglutaryl‑CoA lyase/CrcZ ncRNA
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
RA 5,536,117 C→T V385M (GTG→ATG)  braE ← high‑affinity branched‑chain amino acid ABC transporter permease BraE

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_002947 53196 53237 42 4 [1] [1] 2 opdT‑I tyrosine‑specific outer membrane porin D
* * ÷ NC_002947 97568 97611 44 2 [1] [1] 4 [PP_0090]–[PP_0091] [PP_0090],[PP_0091]
* * ÷ NC_002947 170836 171015–170888 53–180 2 [1] [1] 2 PP_0159/PP_16SA family III CoA‑transferase/16S ribosomal RNA
* * ÷ NC_002947 171392–172965 176285–172973 9–4894 2 [1] [0] 2 [PP_16SA]–[PP_5SA] [PP_16SA],PP_23SA,[PP_5SA]
* * ÷ NC_002947 176673–178395 181690–178403 9–5018 2 [1] [1] 2 PP_16SB–[PP_r01] PP_16SB,PP_23SB,[PP_r01]
* * ÷ NC_002947 353057 353164 108 2 [1] [1] 2 [cbcV] [cbcV]
* * ÷ NC_002947 524151 524212 62 2 [1] [1] 2 tyrS/PP_16SC tyrosine‑‑tRNA ligase/16S ribosomal RNA
* * ÷ NC_002947 547205 547269 65 2 [1] [1] 2 fusA elongation factor G 1
* * ÷ NC_002947 681284 681323 40 2 [1] [1] 2 PP_0583/PP_0584 AraC family transcriptional regulator/methyl‑accepting chemotaxis transducer
* * ÷ NC_002947 796830 796872 43 2 [1] [1] 2 PP_0681/PP_0682 hypothetical protein/inner membrane protein
* * ÷ NC_002947 955129 955159 31 2 [1] [1] 3 cyoE/alaC protoheme IX farnesyltransferase/aminotransferase
* * ÷ NC_002947 1118749 1118814 66 2 [1] [1] 2 [hupN]–[rlmF] [hupN],[rlmF]
* * ÷ NC_002947 1161305 1161323 19 2 [1] [0] 4 PP_1013/yihS sensor histidine kinase/aldose‑ketose isomerase
* * ÷ NC_002947 1388201 1388213 13 2 [1] [1] 5 PP_1204 lipoprotein
* * ÷ NC_002947 1469152 1469170 19 2 [1] [1] 3 algX alginate biosynthesis protein AlgX
* * ÷ NC_002947 1504422 1504440 19 2 [0] [0] 2 trpS/zapE tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein
* * ÷ NC_002947 1717071 1717100 30 3 [1] [1] 2 ppc/adk phosphoenolpyruvate carboxylase/adenylate kinase
* * ÷ NC_002947 2009956 2009971 16 2 [1] [1] 2 PP_1788 hypothetical protein
* * ÷ NC_002947 2012037 2012038 2 3 [0] [1] 2 PP_1790 acylneuraminate cytidylyltransferase
* * ÷ NC_002947 2012389 2012448 60 2 [1] [0] 2 PP_1791 aldolase/synthase
* * ÷ NC_002947 2133516 2133533 18 2 [0] [0] 2 PP_1887/PP_1888 hypothetical protein/fimbrial protein
* * ÷ NC_002947 2300823 2300854 32 2 [0] [1] 2 PP_5496/PP_2023 hypothetical protein/glutathione S‑transferase family protein
* * ÷ NC_002947 2405505 2405532 28 2 [1] [1] 2 evgA/dgt two‑component system response regulator/deoxyguanosinetriphosphate triphosphohydrolase‑like protein
* * ÷ NC_002947 2434918 2434924 7 3 [0] [1] 3 PP_2129/PP_2130 hypothetical protein/lytic transglycosylase
* * ÷ NC_002947 2479142 2479145 4 11 [1] [0] 3 PP_2167/tal PhoD‑like phosphatase/transaldolase
* * ÷ NC_002947 2603739 2603836 98 2 [1] [1] 2 PP_2277 hypothetical protein
* * ÷ NC_002947 2605258 2605303 46 3 [1] [1] 2 [PP_2278]–[PP_5512] [PP_2278],[PP_5512]
* * ÷ NC_002947 3058186 3058282 97 2 [1] [1] 5 [PP_2664]–[agmR] [PP_2664],[agmR]
* * ÷ NC_002947 3471813 3471862 50 2 [1] [1] 2 [PP_3081] [PP_3081]
* * ÷ NC_002947 3781351 3781387 37 2 [0] [0] 2 PP_3338/PP_3339 cytochrome bd‑type quinol oxidase/hypothetical protein
* * ÷ NC_002947 4108039 4108115 77 2 [1] [1] 4 PP_3611 hypothetical protein
* * ÷ NC_002947 4175163 4175189 27 2 [1] [1] 5 katG/PP_3669 catalase‑peroxidase/LysR family transcriptional regulator
* * ÷ NC_002947 4185409 4185448 40 2 [1] [1] 2 PP_3678 hypothetical protein
* * ÷ NC_002947 4205142 4205170 29 2 [1] [1] 3 PP_3690 hypothetical protein
* * ÷ NC_002947 4223292 4223311 20 2 [1] [1] 2 PP_3698 hypothetical protein
* * ÷ NC_002947 4328156 4328206 51 2 [1] [1] 2 PP_3792/PP_5631 hypothetical protein/hypothetical protein
* * ÷ NC_002947 4343468 4343500 33 2 [1] [1] 2 PP_3812/PP_5632 lipase/allo‑isoleucine metabolism protein
* * ÷ NC_002947 4358176 4358191 16 3 [0] [0] 8 yrpB 2‑nitropropane dioxygenase
* * ÷ NC_002947 4535011 4535021 11 2 [1] [0] 4 PP_4018/topB acetyltransferase/DNA topoisomerase III
* * ÷ NC_002947 4680327 4680376 50 2 [1] [0] 3 PP_4137/chrR outer membrane siderophore receptor/chromate reductase
* * ÷ NC_002947 4732158 4732234 77 2 [1] [1] 2 brnQ branched‑chain amino acid transporter
* * ÷ NC_002947 4745808 4745849 42 2 [1] [1] 2 gltA/yeiW citrate synthase/putative oxidoreductase
* * ÷ NC_002947 4801611 4801639 29 2 [0] [1] 2 pvdH/PP_4224 diaminobutyrate‑2‑oxoglutarate transaminase/sensor histidine kinase
* * ÷ NC_002947 4857448 4857453 6 33 [0] [1] 2 recR/ybaB recombination protein RecR/nucleoid‑associated broad specificity regulator
* * ÷ NC_002947 4901424 4901437 14 2 [1] [1] 2 PP_4304/sbp‑I VIC family cation transporter/sulfate ABC transporter substrate‑binding protein
* * ÷ NC_002947 4976403 4976440 38 2 [0] [1] 2 PP_4379 3‑oxoacyl‑ACP synthase
* * ÷ NC_002947 5061900 5062020 121 2 [1] [1] 2 ooxA opine oxidase subunit A
* * ÷ NC_002947 5102216 5102237 22 3 [1] [1] 2 PP_mr66/acsA‑I P6/acetyl‑CoA synthetase
* * ÷ NC_002947 5164783 5164799 17 2 [1] [0] 2 PP_4542/PP_4543 ABC transporter ATP‑binding protein/permease/hypothetical protein
* * ÷ NC_002947 5178232 5178248 17 2 [1] [1] 2 fadD‑I/fadD‑II long‑chain‑fatty acid‑‑CoA ligase/long‑chain‑fatty acid‑‑CoA ligase
* * ÷ NC_002947 5197757 5197768 12 2 [0] [1] 3 PP_4572/PP_4573 hypothetical protein/AAA family ATPase
* * ÷ NC_002947 5204630 5204663 34 2 [0] [1] 2 PP_4579/PP_4580 LysR family transcriptional regulator/hypothetical protein
* * ÷ NC_002947 5261808 5261877 70 2 [1] [1] 2 [PP_5703] [PP_5703]
* * ÷ NC_002947 5349466 5349526 61 2 [1] [1] 2 pgi‑II/acsA‑II glucose 6‑phosphate isomerase/acetyl‑CoA synthetase
* * ÷ NC_002947 5490147 5490199 53 3 [1] [1] 6 purH/purD bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase/phosphoribosylamine‑‑glycine ligase
* * ÷ NC_002947 5511542 5511583 42 2 [1] [0] 2 PP_4839/cycA iron‑regulated membrane protein/D‑alanine/beta‑alanine/D‑serine/glycine permease
* * ÷ NC_002947 5542026 5542097 72 2 [1] [1] 2 nadE/PP_4870 NH(3)‑dependent NAD(+) synthetase/azurin
* * ÷ NC_002947 5660623 5660652 30 4 [1] [1] 2 epd/tktA D‑erythrose 4‑phosphate dehydrogenase/transketolase A
* * ÷ NC_002947 5745481 5745484 4 2 [1] [1] 2 hutF/PP_5037 formiminoglutamate deiminase/lipocalin family lipoprotein
* * ÷ NC_002947 5756731 5756748 18 3 [1] [1] 2 thiI/glnA tRNA sulfurtransferase/glutamine synthetase
* * ÷ NC_002947 5902765 5902801 37 2 [1] [1] 2 PP_5172/PP_5173 hypothetical protein/RND family transporter
* * ÷ NC_002947 6011580 6011591 12 5 [1] [0] 21 ydcJ/PP_5261 metalloprotein/LysR family transcriptional regulator
* * ÷ NC_002947 6018847 6018870 24 6 [1] [1] 3 xpt/PP_5266 xanthine phosphoribosyltransferase/acetyl‑CoA hydrolase family protein
* * ÷ NC_002947 6032902 6032924 23 2 [1] [0] 2 PP_5277/kauB MFS transporter/4‑guanidinobutyraldehyde dehydrogenase
* * ÷ NC_002947 6103418 6103422 5 2 [0] [1] 2 PP_5350 RpiR family transcriptional regulator
* * ÷ NC_002947 6132705 6132711 7 2 [0] [0] 2 PP_5375 LysR family transcriptional regulator
* * ÷ NC_002947 6134250 6134292 43 2 [1] [1] 2 PP_5377 hypothetical protein
* * ÷ NC_002947 6182491 6182525 35 2 [1] [0] 2 atpG/atpA ATP synthase subunit gamma/ATP synthase subunit alpha

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_002947 = 65278661 (1.640)9 (0.240) 5/264 1.3 21.9% coding (1960/1962 nt) ctpL methyl‑accepting chemotaxis protein CtpL
?NC_002947 = 4813152 3 (0.080)intergenic (‑267/‑288) PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
* ? NC_002947 744925 =NA (NA)22 (0.600) 18/262 0.4 84.7% intergenic (‑587/+44) PP_0636/PP_0637 cold shock DNA‑binding domain‑containing protein/transposase
?NC_002947 1015813 = 4 (0.110)intergenic (‑40/‑728) SBRG_Ecoli_galE/prfC SBRG_Ecoli_galE/peptide chain release factor 3
* ? NC_002947 = 746963NA (NA)9 (0.240) 9/262 0.8 100% intergenic (‑87/‑707) PP_0638/PP_5448 transposase/hypothetical protein
?NC_002947 = 1015822 0 (0.000)intergenic (‑49/‑719) SBRG_Ecoli_galE/prfC SBRG_Ecoli_galE/peptide chain release factor 3
* ? NC_002947 = 14245333 (0.080)9 (0.320) 3/200 1.4 71.2% intergenic (‑67/+70) PP_1242/PP_1244 hypothetical protein/hypothetical protein
?NC_002947 = 1424563 5 (0.180)intergenic (‑97/+40) PP_1242/PP_1244 hypothetical protein/hypothetical protein
* ? NC_002947 1849125 =2 (0.050)58 (1.620) 30/254 0.1 95.1% coding (660/2754 nt) gacS sensor protein GacS
?NC_002947 = 2184368 4 (0.110)intergenic (+175/+93) PP_1931/PP_5486 hypothetical protein/hypothetical protein
* ? NC_002947 = 18491282 (0.050)26 (0.720) 19/256 0.3 88.2% coding (657/2754 nt) gacS sensor protein GacS
?NC_002947 2182694 = 5 (0.140)intergenic (+103/‑63) PP_5485/PP_1931 GNAT family acetyltransferase/hypothetical protein
* ? NC_002947 2477094 =3 (0.080)5 (0.190) 5/186 1.0 58.5% intergenic (+6/+143) PP_2166/PP_2167 anti‑anti‑sigma factor/PhoD‑like phosphatase
?NC_002947 2477218 = 5 (0.190)intergenic (+130/+19) PP_2166/PP_2167 anti‑anti‑sigma factor/PhoD‑like phosphatase
* ? NC_002947 = 24771073 (0.080)3 (0.090) 3/250 1.5 24.1% intergenic (+19/+130) PP_2166/PP_2167 anti‑anti‑sigma factor/PhoD‑like phosphatase
?NC_002947 2477305 = 16 (0.460)coding (1783/1851 nt) PP_2167 PhoD‑like phosphatase
* ? NC_002947 = 24771323 (0.080)3 (0.100) 3/218 1.4 34.3% intergenic (+44/+105) PP_2166/PP_2167 anti‑anti‑sigma factor/PhoD‑like phosphatase
?NC_002947 = 4329770 9 (0.290)intergenic (+142/+125) pbpG/PP_3795 murein D‑alanyl‑D‑alanine endopeptidase/hypothetical protein
* ? NC_002947 = 48131732 (0.050)51 (1.510) 10/240 0.7 44.6% intergenic (‑288/‑267) PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
?NC_002947 5993770 = 125 (3.710)intergenic (+59/‑487) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA