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 1,011,323 +T intergenic (‑258/+192) PP_0871 ← / ← SBRG_Ecoli_galM glycine betaine/carnitine/choline ABC transporter permease/SBRG_Ecoli_galM
RA 1,167,912 +A coding (725/1344 nt) oprB‑I → carbohydrate‑selective porin
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 4,746,222 +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 171375–176275 176275 1–4901 6 [5] [5] 6 PP_16SA–[PP_5SA] PP_16SA,PP_23SA,[PP_5SA]
* * ÷ NC_002947 176678–181679 181679 1–5002 6 [2] [5] 6 PP_16SB–[PP_r01] PP_16SB,PP_23SB,[PP_r01]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_002947 336209 =11 (0.410)4 (0.180) 3/240 2.9 32.0% intergenic (+54/+339) PP_0278/PP_0279 hypothetical protein/hypothetical protein
?NC_002947 336329 = 8 (0.360)intergenic (+174/+219) PP_0278/PP_0279 hypothetical protein/hypothetical protein
* ? NC_002947 478264 =17 (0.630)3 (0.140) 3/234 2.8 21.8% intergenic (+9/+101) PP_0393/cca 2‑amino‑4‑hydroxy‑6‑ hydroxymethyldihydropteridine pyrophosphokinase/multifunctional tRNA nucleotidyltransferase/2',3'‑cyclic phosphodiesterase/2' nucleotidase/phosphatase
?NC_002947 478359 = 8 (0.370)intergenic (+104/+6) PP_0393/cca 2‑amino‑4‑hydroxy‑6‑ hydroxymethyldihydropteridine pyrophosphokinase/multifunctional tRNA nucleotidyltransferase/2',3'‑cyclic phosphodiesterase/2' nucleotidase/phosphatase
* ? NC_002947 742918 =NA (NA)7 (0.270) 6/282 2.2 NA coding (1016/1422 nt) PP_0635 group II intron‑encoding maturase
?NC_002947 742948 = NA (NA)coding (1046/1422 nt) PP_0635 group II intron‑encoding maturase
* ? NC_002947 1015848 =0 (0.000)30 (1.120) 25/292 0.1 67.4% intergenic (‑75/‑693) SBRG_Ecoli_galE/prfC SBRG_Ecoli_galE/peptide chain release factor 3
?NC_002947 5066251 = 29 (1.080)intergenic (‑421/‑70) PP_4458/PP_4459 opine ABC transporter substrate‑binding protein/transposase
* ? NC_002947 = 10158541 (0.040)19 (0.730) 18/284 0.4 66.7% intergenic (‑81/‑687) SBRG_Ecoli_galE/prfC SBRG_Ecoli_galE/peptide chain release factor 3
?NC_002947 = 5067412 18 (0.690)coding (1092/1098 nt) PP_4459 transposase
* ? NC_002947 1154932 =20 (0.740)6 (0.240) 5/270 2.4 29.7% intergenic (‑224/+33) PP_1008/gapA RNA polymerase subunit sigma‑24/glyceraldehyde‑3‑phosphate dehydrogenase
?NC_002947 = 2076208 10 (0.400)intergenic (+168/+59) PP_1846/PP_1847 group II intron‑encoding maturase/TonB‑dependent ferric siderophore receptor
* ? NC_002947 1424502 =5 (0.180)5 (0.240) 3/230 2.8 50.2% intergenic (‑36/+101) PP_1242/PP_1244 hypothetical protein/hypothetical protein
?NC_002947 1424596 = 6 (0.280)intergenic (‑130/+7) PP_1242/PP_1244 hypothetical protein/hypothetical protein
* ? NC_002947 = 14245335 (0.180)7 (0.330) 3/230 2.8 58.6% intergenic (‑67/+70) PP_1242/PP_1244 hypothetical protein/hypothetical protein
?NC_002947 = 1424563 6 (0.280)intergenic (‑97/+40) PP_1242/PP_1244 hypothetical protein/hypothetical protein
* ? NC_002947 1491962 =21 (0.780)4 (0.190) 3/234 2.8 23.7% intergenic (+22/+108) yhdZ/degS amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS
?NC_002947 1492052 = 9 (0.420)intergenic (+112/+18) yhdZ/degS amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS
* ? NC_002947 1504392 =13 (0.480)5 (0.220) 4/248 2.6 38.5% intergenic (+13/‑153) trpS/zapE tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein
?NC_002947 1504475 = 5 (0.220)intergenic (+96/‑70) trpS/zapE tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein
* ? NC_002947 = 19721696 (0.220)3 (0.140) 3/228 2.8 26.5% intergenic (+47/+72) PP_1762/yciK hypothetical protein/putative oxidoreductase
?NC_002947 = 1972199 12 (0.570)intergenic (+77/+42) PP_1762/yciK hypothetical protein/putative oxidoreductase
* ? NC_002947 = 206281513 (0.480)3 (0.130) 3/246 3.0 20.1% intergenic (+39/+89) PP_1832/PP_1833 oxidase/hypothetical protein
?NC_002947 = 2062855 13 (0.570)intergenic (+79/+49) PP_1832/PP_1833 oxidase/hypothetical protein
* ? NC_002947 = 2091242NA (NA)4 (0.160) 4/278 2.9 NA coding (365/1302 nt) PP_1865 transposase
?NC_002947 = 2091288 NA (NA)coding (411/1302 nt) PP_1865 transposase
* ? NC_002947 = 224192616 (0.590)5 (0.210) 5/262 2.4 28.4% intergenic (+29/+99) uvrB/PP_1975 uvrABC excinuclease protein B/EmrB/QacA family drug resistance transporter
?NC_002947 = 2241985 11 (0.460)intergenic (+88/+40) uvrB/PP_1975 uvrABC excinuclease protein B/EmrB/QacA family drug resistance transporter
* ? NC_002947 2477094 =6 (0.220)3 (0.150) 3/216 2.6 48.4% intergenic (+6/+143) PP_2166/PP_2167 anti‑anti‑sigma factor/PhoD‑like phosphatase
?NC_002947 2477218 = 2 (0.100)intergenic (+130/+19) PP_2166/PP_2167 anti‑anti‑sigma factor/PhoD‑like phosphatase
* ? NC_002947 = 279990223 (0.850)8 (0.300)
+T
6/292 2.3 24.4% intergenic (+18/+94) PP_2447/puuB hypothetical protein/gamma‑glutamylputrescine oxidase
?NC_002947 = 2799976 27 (1.000)intergenic (+92/+20) PP_2447/puuB hypothetical protein/gamma‑glutamylputrescine oxidase
* ? NC_002947 4164076 =23 (0.850)7 (0.290) 4/262 2.7 31.5% intergenic (+31/‑178) PP_3661/PP_3662 membrane protein/hypothetical protein
?NC_002947 4164136 = 10 (0.410)intergenic (+91/‑118) PP_3661/PP_3662 membrane protein/hypothetical protein
* ? NC_002947 4529388 =18 (0.670)7 (0.290) 5/266 2.4 31.6% intergenic (+18/‑175) idh/PP_4013 isocitrate dehydrogenase/MutT/nudix family protein
?NC_002947 4529423 = 14 (0.570)intergenic (+53/‑140) idh/PP_4013 isocitrate dehydrogenase/MutT/nudix family protein
* ? NC_002947 4591012 =11 (0.410)5 (0.250) 5/218 1.9 49.6% intergenic (+102/+115) PP_4061/PP_4063 hypothetical protein/long‑chain fatty acid‑‑CoA ligase
?NC_002947 4591116 = 2 (0.100)intergenic (+206/+11) PP_4061/PP_4063 hypothetical protein/long‑chain fatty acid‑‑CoA ligase
* ? NC_002947 4652552 =2 (0.070)4 (0.200) 3/216 2.6 51.7% intergenic (+10/+121) fusB/PP_4112 elongation factor G 2/sulfate transporter
?NC_002947 4652660 = 6 (0.300)intergenic (+118/+13) fusB/PP_4112 elongation factor G 2/sulfate transporter
* ? NC_002947 = 46525902 (0.070)6 (0.300) 5/216 1.9 61.6% intergenic (+48/+83) fusB/PP_4112 elongation factor G 2/sulfate transporter
?NC_002947 = 4652620 6 (0.300)intergenic (+78/+53) fusB/PP_4112 elongation factor G 2/sulfate transporter
* ? NC_002947 4813167 =0 (0.000)6 (0.220) 4/290 3.0 38.7% intergenic (‑282/‑273) PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
?NC_002947 = 4950366 19 (0.710)intergenic (+732/+66) PP_5673/flhB D‑alanine‑‑D‑alanine ligase/flagellin export apparatus substrate specificity protein
* ? NC_002947 = 48131732 (0.070)13 (0.520) 11/270 1.1 52.2% intergenic (‑288/‑267) PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
?NC_002947 5993770 = 22 (0.890)intergenic (+59/‑487) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
* ? NC_002947 5133802 =18 (0.670)6 (0.230) 5/278 2.5 27.3% coding (300/438 nt) PP_4515 MarR family transcriptional regulator
?NC_002947 5133835 = 15 (0.590)coding (267/438 nt) PP_4515 MarR family transcriptional regulator
* ? NC_002947 5316377 =NA (NA)5 (0.190) 4/280 2.9 100% noncoding (1302/1522 nt) PP_16SG 16S ribosomal RNA
?NC_002947 5316385 = 0 (0.000)noncoding (1294/1522 nt) PP_16SG 16S ribosomal RNA
* ? NC_002947 = 538742910 (0.370)4 (0.190) 3/224 2.7 32.5% intergenic (+52/+81) smpB/pdhR SsrA‑binding protein/DNA‑binding transcriptional regulator LldR
?NC_002947 = 5387457 9 (0.440)intergenic (+80/+53) smpB/pdhR SsrA‑binding protein/DNA‑binding transcriptional regulator LldR
* ? NC_002947 = 566059719 (0.700)6 (0.230) 5/280 2.5 21.4% intergenic (‑52/+100) epd/tktA D‑erythrose 4‑phosphate dehydrogenase/transketolase A
?NC_002947 = 5660674 26 (1.010)intergenic (‑129/+23) epd/tktA D‑erythrose 4‑phosphate dehydrogenase/transketolase A
* ? NC_002947 5739035 =16 (0.590)6 (0.240) 6/270 2.1 29.5% intergenic (‑56/+101) proY/hutH proline (histidine) APC transporter/histidine ammonia‑lyase
?NC_002947 5739114 = 14 (0.560)intergenic (‑135/+22) proY/hutH proline (histidine) APC transporter/histidine ammonia‑lyase
* ? NC_002947 5748341 =12 (0.440)10 (0.410) 5/268 2.4 52.7% intergenic (‑169/+78) fbp/glgP class 1 fructose‑1,6‑bisphosphatase/glycogen phosphorylase
?NC_002947 5748395 = 7 (0.280)intergenic (‑223/+24) fbp/glgP class 1 fructose‑1,6‑bisphosphatase/glycogen phosphorylase
* ? NC_002947 5821859 =16 (0.590)6 (0.250) 5/258 2.3 32.4% intergenic (+40/+89) PP_5092/pilT NLP/P60 protein/twitching motility protein
?NC_002947 5821922 = 11 (0.460)intergenic (+103/+26) PP_5092/pilT NLP/P60 protein/twitching motility protein
* ? NC_002947 5919162 =13 (0.480)5 (0.230) 3/238 2.9 29.0% intergenic (+49/+104) spuI/argA glutamylpolyamine synthetase/amino acid N‑acetyltransferase
?NC_002947 5919258 = 14 (0.640)intergenic (+145/+8) spuI/argA glutamylpolyamine synthetase/amino acid N‑acetyltransferase
* ? NC_002947 = 600593711 (0.410)3 (0.140) 3/234 2.8 21.6% intergenic (+39/+70) PP_5256/amaA cyclic nucleotide‑binding protein/L‑pipecolate oxidase
?NC_002947 = 6005971 13 (0.600)intergenic (+73/+36) PP_5256/amaA cyclic nucleotide‑binding protein/L‑pipecolate oxidase