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 1,484,303 T→G V125G (GTC→GGC)  yhdX → amino acid ABC transporter permease
JC 1,843,229 (GCGCCAGTTCGTGGC)1→2 coding (1607/2754 nt) gacS ← sensor protein GacS
MC JC 1,930,434 Δ63 bp [apeB] [apeB]
RA 3,823,901 +T coding (1248/1293 nt) kguT ← 2‑ketogluconate transporter, putative
RA 3,824,415 A→G I245T (ATC→ACC)  kguT ← 2‑ketogluconate transporter, putative
MC JC 3,827,335 Δ51 bp coding (626‑676/1020 nt) ptxS ← 2‑ketogluconate utilization repressor
RA 4,160,437 A→C S161R (AGC→CGC)  PP_3661 → membrane protein
RA 4,743,195 +C intergenic (+464/+288) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,743,197 A→G intergenic (+466/+286) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,743,199 C→T intergenic (+468/+284) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,743,202 C→T intergenic (+471/+281) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,743,205 C→G intergenic (+474/+278) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,743,207 2 bp→CT intergenic (+476/+275) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,743,221 C→T intergenic (+490/+262) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,743,223 A→C intergenic (+492/+260) gltA → / ← yeiW citrate synthase/putative oxidoreductase
RA 4,743,226 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 19502 19566 65 2 [1] [1] 3 PP_0015 transposon protein
* * ÷ NC_002947 20797 20933 137 2 [1] [1] 2 PP_0016 hypothetical protein
* * ÷ NC_002947 22872 22959 88 2 [0] [1] 2 PP_0017/PP_0018 transcriptional regulator/hypothetical protein
* * ÷ NC_002947 23343 23377 35 2 [1] [1] 3 PP_0018 hypothetical protein
* * ÷ NC_002947 23813 23929 117 3 [1] [1] 2 PP_0018 hypothetical protein
* * ÷ NC_002947 34709 34722 14 2 [1] [0] 2 czrSA metal‑sensor histidine kinase
* * ÷ NC_002947 35314 35366 53 2 [1] [1] 2 PP_0031 hypothetical protein
* * ÷ NC_002947 43411 43449 39 2 [1] [1] 2 [PP_0040] [PP_0040]
* * ÷ NC_002947 97568 97611 44 2 [1] [1] 5 [PP_0090]–[PP_0091] [PP_0090],[PP_0091]
* * ÷ NC_002947 170836 170848 13 2 [0] [1] 2 PP_0159/PP_16SA family III CoA‑transferase/16S ribosomal RNA
* * ÷ NC_002947 171390–176316 176316 1–4927 2 [1] [1] 2 [PP_16SA]–[PP_5SA] [PP_16SA],PP_23SA,[PP_5SA]
* * ÷ NC_002947 176645–181722 181722 1–5078 2 [1] [1] 2 PP_16SB–[PP_r01] PP_16SB,PP_23SB,[PP_r01]
* * ÷ NC_002947 353059 353115 57 2 [1] [1] 2 hisF/cbcV imidazole glycerol phosphate synthase subunit HisF/choline/betaine/carnitine ABC transporter ATP binding protein
* * ÷ NC_002947 524170 524205 36 2 [1] [1] 3 tyrS/PP_16SC tyrosine‑‑tRNA ligase/16S ribosomal RNA
* * ÷ NC_002947 536776 536854 79 2 [1] [1] 2 rplJ 50S ribosomal protein L10
* * ÷ NC_002947 614283 614321 39 2 [1] [1] 3 dxs/ispA 1‑deoxyxylulose‑5‑phosphate synthase/farnesyl diphosphate synthase
* * ÷ NC_002947 681289 681307 19 2 [1] [0] 2 PP_0583/PP_0584 AraC family transcriptional regulator/methyl‑accepting chemotaxis transducer
* * ÷ NC_002947 718452 718476 25 2 [1] [1] 2 thiO/PP_0613 FAD‑dependent glycine/D‑amino acid oxidase/amidase family protein
* * ÷ NC_002947 883871 883889 19 2 [0] [1] 2 PP_0766/PP_0767 hypothetical protein/LuxR family transcriptional regulator
* * ÷ NC_002947 955141 955159 19 2 [1] [0] 2 cyoE/alaC protoheme IX farnesyltransferase/aminotransferase
* * ÷ NC_002947 1114923 1114941 19 3 [0] [0] 2 rlmF/valS ribosomal RNA large subunit methyltransferase F/valine‑‑tRNA ligase
* * ÷ NC_002947 1156332 1156359 28 2 [1] [0] 2 PP_1013/yihS sensor histidine kinase/aldose‑ketose isomerase
* * ÷ NC_002947 1367700 1367749 50 2 [1] [1] 3 PP_1193 membrane protein
* * ÷ NC_002947 1419584 1419591 8 2 [0] [0] 2 PP_1242/PP_1244 hypothetical protein/hypothetical protein
* * ÷ NC_002947 1499473 1499498 26 3 [1] [1] 2 trpS/zapE tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein
* * ÷ NC_002947 1592635 1592672 38 2 [1] [0] 4 PP_1397 hypothetical protein
* * ÷ NC_002947 1639610 1639660 51 3 [1] [1] 6 czcR‑III/PP_1439 response regulator/hypothetical protein
* * ÷ NC_002947 1921576 1921607 32 3 [1] [1] 4 PP_1720/PP_1721 alcohol dehydrogenase/phosphoserine phosphatase
* * ÷ NC_002947 1970805 1970823 19 2 [1] [0] 2 mtnA/PP_mr25 methylthioribose‑1‑phosphate isomerase/gyrA regulatory region
* * ÷ NC_002947 2003395 2003516 122 2 [1] [1] 2 PP_1786 glycosyl transferase
* * ÷ NC_002947 2006704 2006782 79 2 [1] [1] 2 [PP_1789]–[PP_1790] [PP_1789],[PP_1790]
* * ÷ NC_002947 2187079 2187211 133 2 [0] [1] 2 PP_1936 membrane protein
* * ÷ NC_002947 2187937 2187961 25 3 [0] [1] 2 PP_1936 membrane protein
* * ÷ NC_002947 2188196 2188207 12 2 [0] [1] 2 PP_1936 membrane protein
* * ÷ NC_002947 2192366 2192409 44 2 [1] [0] 3 PP_1937 helicase
* * ÷ NC_002947 2203387 2203444 58 2 [1] [0] 2 PP_1946 short‑chain dehydrogenase/reductase family oxidoreductase
* * ÷ NC_002947 2222641 2222692 52 2 [1] [0] 2 PP_1960 hypothetical protein
* * ÷ NC_002947 2297796 2297823 28 8 [0] [1] 2 PP_5496/PP_2023 hypothetical protein/glutathione S‑transferase family protein
* * ÷ NC_002947 3055154 3055211 58 4 [0] [1] 2 [PP_2664]–[agmR] [PP_2664],[agmR]
* * ÷ NC_002947 3468792 3468817 26 2 [0] [0] 3 PP_3081/PP_5560 hypothetical protein/hypothetical protein
* * ÷ NC_002947 3778314 3778379 66 2 [0] [0] 2 PP_3338/PP_3339 cytochrome bd‑type quinol oxidase/hypothetical protein
* * ÷ NC_002947 3953052 3953070 19 2 [1] [0] 2 PP_3486/PP_3487 cytochrome c/hypothetical protein
* * ÷ NC_002947 4051876 4051888 13 3 [0] [1] 2 quiA/oprB‑III quinate dehydrogenase/carbohydrate‑selective porin
* * ÷ NC_002947 4081443 4081473 31 2 [1] [1] 5 sdaC/amaC serine:H+ symport permease/D‑lysine aminotransferase
* * ÷ NC_002947 4172144 4172157 14 2 [1] [0] 2 katG/PP_3669 catalase‑peroxidase/LysR family transcriptional regulator
* * ÷ NC_002947 4184621 4184695 75 4 [1] [1] 2 PP_3680 hypothetical protein
* * ÷ NC_002947 4206232 4206333 102 2 [1] [1] 2 PP_3691 DNA helicase‑related protein
* * ÷ NC_002947 4212977 4212993 17 2 [1] [1] 3 PP_5621 hypothetical protein
* * ÷ NC_002947 4214257 4214402 146 2 [1] [1] 2 PP_3694 hypothetical protein
* * ÷ NC_002947 4223436 4223532 97 2 [1] [1] 2 PP_3700 chromosome partitioning ATPase
* * ÷ NC_002947 4226551 4226598 48 2 [0] [1] 2 PP_3703/PP_3704 hypothetical protein/hypothetical protein
* * ÷ NC_002947 4229540 4229627 88 2 [1] [1] 2 PP_3706 hypothetical protein
* * ÷ NC_002947 4355149 4355164 16 2 [1] [1] 6 yrpB 2‑nitropropane dioxygenase
* * ÷ NC_002947 4677277 4677338 62 4 [1] [1] 2 PP_4137/chrR outer membrane siderophore receptor/chromate reductase
* * ÷ NC_002947 4742773 4742824 52 2 [0] [1] 2 gltA/yeiW citrate synthase/putative oxidoreductase
* * ÷ NC_002947 4798556 4798590 35 2 [1] [0] 3 pvdH/PP_4224 diaminobutyrate‑2‑oxoglutarate transaminase/sensor histidine kinase
* * ÷ NC_002947 4810147 4810175 29 36 [0] [0] 10 PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
* * ÷ NC_002947 4844864 4844868 5 2 [1] [0] 2 ccoP‑II/PP_4259 cbb3‑type cytochrome c oxidase subunit/iron‑sulfur cluster‑binding protein
* * ÷ NC_002947 4854421 4854447 27 5 [0] [1] 2 recR/ybaB recombination protein RecR/nucleoid‑associated broad specificity regulator
* * ÷ NC_002947 4952923 4952960 38 2 [1] [1] 2 fliL/fliK flagellar protein FliL/flagellar hook‑length control protein FliK
* * ÷ NC_002947 5029647 5029732 86 3 [1] [1] 3 [ocd]–[PP_4432] [ocd],[PP_4432]
* * ÷ NC_002947 5030388 5030417 30 2 [1] [1] 2 PP_4432 Xaa‑Pro aminopeptidase
* * ÷ NC_002947 5058733 5058846 114 2 [1] [1] 2 ooxA opine oxidase subunit A
* * ÷ NC_002947 5065530 5065615 86 2 [1] [1] 2 PP_4460/PP_4461 LysR family transcriptional regulator/MFS transporter
* * ÷ NC_002947 5068031 5068054 24 3 [1] [1] 2 PP_4463 carbon‑nitrogen hydrolase family protein
* * ÷ NC_002947 5069713 5069733 21 2 [1] [1] 2 PP_4464/PP_4465 LysR family transcriptional regulator/porin
* * ÷ NC_002947 5070666 5070785 120 2 [1] [1] 2 PP_4465 porin
* * ÷ NC_002947 5099205 5099219 15 2 [1] [0] 2 PP_mr66/acsA‑I P6/acetyl‑CoA synthetase
* * ÷ NC_002947 5201613 5201658 46 2 [0] [1] 2 PP_4579/PP_4580 LysR family transcriptional regulator/hypothetical protein
* * ÷ NC_002947 5258830 5258845 16 2 [1] [1] 2 PP_5703/PP_4634 type III effector protein HopJ/alpha/beta family hydrolase
* * ÷ NC_002947 5487097 5487128 32 3 [1] [1] 2 purH/purD bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase/phosphoribosylamine‑‑glycine ligase
* * ÷ NC_002947 5508537 5508565 29 4 [0] [1] 2 PP_4839/cycA iron‑regulated membrane protein/D‑alanine/beta‑alanine/D‑serine/glycine permease
* * ÷ NC_002947 6100358 6100390 33 7 [0] [0] 2 PP_5350 RpiR family transcriptional regulator
* * ÷ NC_002947 6162520 6162564 45 2 [0] [1] 2 PP_5740 hypothetical protein
* * ÷ NC_002947 6163716 6163722 7 2 [1] [0] 2 PP_5403 hypothetical protein
* * ÷ NC_002947 6183852 6183858 7 21 [0] [0] NA atpI/– ATP synthase protein I/–

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_002947 1 =0 (0.000)21 (0.540) 16/264 0.6 100% intergenic (–/+146) –/parB –/chromosome‑partitioning protein
?NC_002947 = 6183851 0 (0.000)intergenic (‑3/–) atpI/– ATP synthase protein I/–
* ? NC_002947 = 65278635 (0.900)19 (0.490) 3/264 2.4 52.0% coding (1960/1962 nt) ctpL methyl‑accepting chemotaxis protein CtpL
?NC_002947 = 4810125 0 (0.000)intergenic (‑267/‑288) PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
* ? NC_002947 = 65278635 (0.900)6 (0.210) 4/194 1.7 31.8% coding (1960/1962 nt) ctpL methyl‑accepting chemotaxis protein CtpL
?NC_002947 4810176 = 0 (0.000)intergenic (‑318/‑237) PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
* ? NC_002947 1617825 =20 (0.520)12 (0.350) 9/234 1.1 43.9% intergenic (‑38/+135) PP_1417/PP_1418 tricarboxylate transport protein TctB/tricarboxylate transport protein TctC
?NC_002947 1617914 = 13 (0.380)intergenic (‑127/+46) PP_1417/PP_1418 tricarboxylate transport protein TctB/tricarboxylate transport protein TctC
* ? NC_002947 2474067 =5 (0.130)3 (0.110) 3/186 1.9 34.2% intergenic (+6/+143) PP_2166/PP_2167 anti‑anti‑sigma factor/PhoD‑like phosphatase
?NC_002947 2474191 = 8 (0.290)intergenic (+130/+19) PP_2166/PP_2167 anti‑anti‑sigma factor/PhoD‑like phosphatase
* ? NC_002947 = 24740805 (0.130)3 (0.080) 3/250 2.3 21.6% intergenic (+19/+130) PP_2166/PP_2167 anti‑anti‑sigma factor/PhoD‑like phosphatase
?NC_002947 2474278 = 17 (0.460)coding (1783/1851 nt) PP_2167 PhoD‑like phosphatase
* ? NC_002947 = 48101460 (0.000)28 (0.850) 7/224 1.3 59.0% intergenic (‑288/‑267) PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
?NC_002947 = 5990927 39 (1.190)intergenic (+243/‑303) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA