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
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 4,746,232 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

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_002947 171376–176292 176292 1–4917 16 [15] [14] 16 PP_16SA–[PP_5SA] PP_16SA,PP_23SA,[PP_5SA]
* * ÷ NC_002947 176632–181706 181706 1–5075 17 [15] [15] 16 PP_16SB–[PP_r01] PP_16SB,PP_23SB,[PP_r01]
* * ÷ NC_002947 4813154 4813167 14 40 [2] [0] 51 PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_002947 = 176399NA (NA)38 (0.810)
+CGAAA
25/246 1.2 36.4% intergenic (+43/‑420) PP_5SA/PP_16SB 5S ribosomal RNA/16S ribosomal RNA
?NC_002947 = 182013 69 (1.410)intergenic (+2/+63) PP_5SB/PP_0160 5S ribosomal RNA/ferrioxamine receptor
* ? NC_002947 413997 =47 (0.960)15 (0.390) 13/200 2.4 30.4% intergenic (+14/‑189) glnE/waaF glutamate‑ammonia‑ligase adenylyltransferase/ADP‑heptose:LPS heptosyltransferase II
?NC_002947 414083 = 32 (0.840)intergenic (+100/‑103) glnE/waaF glutamate‑ammonia‑ligase adenylyltransferase/ADP‑heptose:LPS heptosyltransferase II
* ? NC_002947 = 65278545 (0.920)31 (0.750) 27/216 0.7 62.1% coding (1961/1962 nt) ctpL methyl‑accepting chemotaxis protein CtpL
?NC_002947 = 4813153 0 (0.000)intergenic (‑268/‑287) PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
* ? NC_002947 1161277 =35 (0.710)15 (0.380) 13/206 2.5 36.5% intergenic (+25/‑191) PP_1013/yihS sensor histidine kinase/aldose‑ketose isomerase
?NC_002947 1161350 = 24 (0.610)intergenic (+98/‑118) PP_1013/yihS sensor histidine kinase/aldose‑ketose isomerase
* ? NC_002947 1301529 =NA (NA)19 (0.420) 20/238 1.7 NA intergenic (‑327/‑239) nhaA‑I/PP_1133 Na(+)/H(+) antiporter NhaA/transposase
?NC_002947 1301565 = NA (NA)intergenic (‑363/‑203) nhaA‑I/PP_1133 Na(+)/H(+) antiporter NhaA/transposase
* ? NC_002947 1491962 =37 (0.750)16 (0.430) 13/196 2.3 44.3% intergenic (+22/+108) yhdZ/degS amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS
?NC_002947 1492052 = 12 (0.320)intergenic (+112/+18) yhdZ/degS amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS
* ? NC_002947 = 210497453 (1.080)15 (0.370) 13/210 2.6 22.8% intergenic (‑93/‑112) PP_1875/PP_1876 two‑component system sensor histidine kinase/response regulator/AAA family ATP/GTP‑binding protein
?NC_002947 = 2105023 58 (1.440)intergenic (‑142/‑63) PP_1875/PP_1876 two‑component system sensor histidine kinase/response regulator/AAA family ATP/GTP‑binding protein
* ? NC_002947 4591012 =17 (0.350)11 (0.320) 11/180 2.4 49.0% intergenic (+102/+115) PP_4061/PP_4063 hypothetical protein/long‑chain fatty acid‑‑CoA ligase
?NC_002947 4591116 = 11 (0.320)intergenic (+206/+11) PP_4061/PP_4063 hypothetical protein/long‑chain fatty acid‑‑CoA ligase
* ? NC_002947 = 459104917 (0.350)14 (0.410) 14/180 1.8 55.0% intergenic (+139/+78) PP_4061/PP_4063 hypothetical protein/long‑chain fatty acid‑‑CoA ligase
?NC_002947 = 4591077 11 (0.320)intergenic (+167/+50) PP_4061/PP_4063 hypothetical protein/long‑chain fatty acid‑‑CoA ligase
* ? NC_002947 4813168 =0 (0.000)24 (0.680) 14/186 1.9 59.3% intergenic (‑283/‑272) PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
?NC_002947 = 5993940 33 (0.930)intergenic (+229/‑317) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
* ? NC_002947 4901372 =40 (0.820)18 (0.440) 16/214 2.0 37.4% intergenic (+11/‑197) PP_4304/sbp‑I VIC family cation transporter/sulfate ABC transporter substrate‑binding protein
?NC_002947 4901461 = 27 (0.660)intergenic (+100/‑108) PP_4304/sbp‑I VIC family cation transporter/sulfate ABC transporter substrate‑binding protein
* ? NC_002947 = 520661214 (0.290)11 (0.320) 10/182 2.7 46.9% intergenic (‑101/‑79) PP_4582/PP_4583 membrane protein/putative Peptidase
?NC_002947 = 5206633 15 (0.430)intergenic (‑122/‑58) PP_4582/PP_4583 membrane protein/putative Peptidase
* ? NC_002947 5338192 =59 (1.200)14 (0.320) 14/226 2.6 22.8% intergenic (+27/‑216) gluQ/PP_5704 glutamyl‑Q tRNA(Asp) synthetase/hypothetical protein
?NC_002947 5338252 = 43 (0.990)intergenic (+87/‑156) gluQ/PP_5704 glutamyl‑Q tRNA(Asp) synthetase/hypothetical protein
* ? NC_002947 5482087 =48 (0.980)19 (0.570) 13/174 1.9 53.9% intergenic (+3/+109) PP_4813/PP_4814 PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein
?NC_002947 5482186 = 0 (0.000)intergenic (+102/+10) PP_4813/PP_4814 PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein
* ? NC_002947 = 554205463 (1.280)14 (0.360) 12/202 2.6 20.6% intergenic (+34/+69) nadE/PP_4870 NH(3)‑dependent NAD(+) synthetase/azurin
?NC_002947 = 5542076 58 (1.500)intergenic (+56/+47) nadE/PP_4870 NH(3)‑dependent NAD(+) synthetase/azurin
* ? NC_002947 = 582187644 (0.900)16 (0.380) 12/220 3.0 26.3% intergenic (+57/+72) PP_5092/pilT NLP/P60 protein/twitching motility protein
?NC_002947 = 5821903 52 (1.240)intergenic (+84/+45) PP_5092/pilT NLP/P60 protein/twitching motility protein
* ? NC_002947 6011544 =29 (0.590)15 (0.430) 11/184 2.5 55.8% intergenic (+7/+92) ydcJ/PP_5261 metalloprotein/LysR family transcriptional regulator
?NC_002947 6011628 = 3 (0.090)intergenic (+91/+8) ydcJ/PP_5261 metalloprotein/LysR family transcriptional regulator