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 1,680,017 T→G T276P (ACC→CCC)  PP_1475 ← CAIB/BAIF family protein
RA 3,824,314 C→G A279P (GCG→CCG)  kguT ← 2‑ketogluconate transporter, putative
RA 3,827,925 G→A S29F (TCC→TTC)  ptxS ← 2‑ketogluconate utilization repressor
RA 4,637,297 A→G S143P (TCT→CCT)  uvrY ← BarA/UvrY two‑componenent system response regulator
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
RA 5,367,766 A→G F254L (TTC→CTC)  ftsH ← integral membrane ATP‑dependent zinc metallopeptidase

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_002947 19666 19919 254 4 [3] [3] 4 PP_0015 transposon protein
* * ÷ NC_002947 20056 20196 141 4 [3] [3] 4 [PP_0015] [PP_0015]
* * ÷ NC_002947 21488 21771 284 4 [3] [3] 4 PP_0016 hypothetical protein
* * ÷ NC_002947 32620 32698 79 4 [2] [3] 4 PP_5422/czcR‑I hypothetical protein/heavy metal two‑component system response regulator
* * ÷ NC_002947 51594 51967 374 4 [3] [3] 4 czcC‑I cobalt‑zinc‑cadmium resistance protein
* * ÷ NC_002947 91767 91844 78 4 [3] [2] 4 trpA tryptophan synthase subunit alpha
* * ÷ NC_002947 97567 97614 48 4 [2] [3] 4 [PP_0090]–[PP_0091] [PP_0090],[PP_0091]
* * ÷ NC_002947 170738 170936–170881 144–199 5 [3] [3] 4 [PP_0159] [PP_0159]
* * ÷ NC_002947 171388–172965 176286–172977 13–4899 4 [3] [3] 4 PP_16SA–[PP_5SA] PP_16SA,PP_23SA,[PP_5SA]
* * ÷ NC_002947 176639–178395 181708–178407 13–5070 8 [3] [3] 4 PP_16SB–[PP_r01] PP_16SB,PP_23SB,[PP_r01]
* * ÷ NC_002947 353090 353145 56 4 [3] [3] 4 hisF/cbcV imidazole glycerol phosphate synthase subunit HisF/choline/betaine/carnitine ABC transporter ATP binding protein
* * ÷ NC_002947 524167 524248 82 4 [2] [3] 5 tyrS/PP_16SC tyrosine‑‑tRNA ligase/16S ribosomal RNA
* * ÷ NC_002947 681269 681323 55 4 [2] [3] 5 PP_0583/PP_0584 AraC family transcriptional regulator/methyl‑accepting chemotaxis transducer
* * ÷ NC_002947 718444 718503 60 5 [3] [3] 4 thiO/PP_0613 FAD‑dependent glycine/D‑amino acid oxidase/amidase family protein
* * ÷ NC_002947 796785 796898 114 4 [3] [3] 5 [PP_0681] [PP_0681]
* * ÷ NC_002947 883837 883918 82 4 [3] [3] 4 PP_0766/PP_0767 hypothetical protein/LuxR family transcriptional regulator
* * ÷ NC_002947 1124531 1124581 51 4 [3] [3] 5 gcvT‑I aminomethyltransferase
* * ÷ NC_002947 1367695 1367756 62 4 [3] [2] 4 PP_1193 membrane protein
* * ÷ NC_002947 1506901 1506990 90 5 [3] [3] 4 petC/sspA ubiquinol‑‑cytochrome c reductase cytochrome c1 subunit/stringent starvation protein A
* * ÷ NC_002947 1592623 1592668 46 4 [3] [3] 4 PP_1397 hypothetical protein
* * ÷ NC_002947 1704663 1704695 33 4 [1] [2] 4 [PP_1499] [PP_1499]
* * ÷ NC_002947 1712100 1712136 37 4 [3] [3] 5 ppc/adk phosphoenolpyruvate carboxylase/adenylate kinase
* * ÷ NC_002947 1921566 1921617 52 5 [2] [3] 4 [PP_1720] [PP_1720]
* * ÷ NC_002947 1932638 1932677 40 4 [3] [1] 4 rluA/minE bifunctional tRNA pseudouridine(32) synthase TrmQ/ribosomal large subunit pseudouridine synthase RluA/cell division topological specificity factor
* * ÷ NC_002947 1947824 1947887 64 5 [2] [3] 4 PP_1748/PP_1749 hypothetical protein/acetyltransferase
* * ÷ NC_002947 2130489 2130506 18 4 [0] [1] 4 PP_1887/PP_1888 hypothetical protein/fimbrial protein
* * ÷ NC_002947 2190426 2190559 134 4 [3] [2] 4 [PP_5491]–[PP_5492] [PP_5491],[PP_5492]
* * ÷ NC_002947 2216426 2216584 159 4 [3] [3] 4 PP_1957 Pdr/VanB family oxidoreductase
* * ÷ NC_002947 2220306 2220621 316 4 [3] [3] 4 [PP_5495] [PP_5495]
* * ÷ NC_002947 2273168 2273224 57 7 [2] [3] 4 PP_2002/PP_t31 oxidoreductase/tRNA‑Val
* * ÷ NC_002947 2297796 2297830 35 7 [2] [2] 5 PP_5496/PP_2023 hypothetical protein/glutathione S‑transferase family protein
* * ÷ NC_002947 2476115 2476118 4 20 [1] [0] 7 PP_2167/tal PhoD‑like phosphatase/transaldolase
* * ÷ NC_002947 2480374 2480442 69 4 [3] [3] 5 PP_2172 hypothetical protein
* * ÷ NC_002947 2839040 2839156 117 4 [3] [3] 4 sad‑I/PP_2489 NAD+‑dependent succinate semialdehyde dehydrogenase/xenobiotic reductase
* * ÷ NC_002947 3055136 3055211 76 4 [3] [2] 5 [PP_2664]–[agmR] [PP_2664],[agmR]
* * ÷ NC_002947 3778324 3778366 43 4 [3] [3] 4 PP_3338/PP_3339 cytochrome bd‑type quinol oxidase/hypothetical protein
* * ÷ NC_002947 3847670 3847713 44 4 [3] [2] 4 [PP_3395] [PP_3395]
* * ÷ NC_002947 3953041 3953120 80 4 [2] [3] 4 PP_3486/PP_3487 cytochrome c/hypothetical protein
* * ÷ NC_002947 4152016 4152057 42 4 [3] [3] 6 PP_3654/PP_3655 leucine‑responsive regulatory protein/cytosine/purine/uracil/thiamine/allantoin permease family protein
* * ÷ NC_002947 4172123 4172174 52 8 [3] [2] 5 katG/PP_3669 catalase‑peroxidase/LysR family transcriptional regulator
* * ÷ NC_002947 4211387 4211637 251 4 [3] [3] 4 PP_3692 hypothetical protein
* * ÷ NC_002947 4212204 4212488 285 4 [3] [3] 4 PP_3692 hypothetical protein
* * ÷ NC_002947 4215976 4216146 171 4 [3] [3] 5 PP_3696 hypothetical protein
* * ÷ NC_002947 4216927 4217103 177 5 [3] [3] 5 PP_3697 hypothetical protein
* * ÷ NC_002947 4217711 4217955 245 4 [3] [3] 4 PP_3697 hypothetical protein
* * ÷ NC_002947 4219514 4220042 529 4 [2] [3] 4 [PP_5622]–[PP_3698] [PP_5622],[PP_3698]
* * ÷ NC_002947 4220205 4220310 106 4 [2] [3] 5 PP_3698 hypothetical protein
* * ÷ NC_002947 4228043 4228156 114 6 [2] [3] 4 [PP_3705] [PP_3705]
* * ÷ NC_002947 4228362 4228786 425 4 [3] [3] 4 PP_5623 membrane protein
* * ÷ NC_002947 4342007 4342061 55 5 [3] [3] 5 ribAB‑II/PP_3814 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein
* * ÷ NC_002947 4355126 4355164 39 7 [2] [0] 4 yrpB 2‑nitropropane dioxygenase
* * ÷ NC_002947 4491727 4492004 278 4 [3] [3] 4 PP_3982 hypothetical protein
* * ÷ NC_002947 4505729 4505761 33 4 [2] [3] 4 xanP/tusD xanthine permease/sulfur transfer protein complex subunit TusD
* * ÷ NC_002947 4531961 4532001 41 8 [3] [1] 4 PP_4018/topB acetyltransferase/DNA topoisomerase III
* * ÷ NC_002947 4742781 4742825 45 6 [3] [2] 4 gltA/yeiW citrate synthase/putative oxidoreductase
* * ÷ NC_002947 5022904 5023028 125 4 [3] [3] 4 PP_4425 amino acid ABC transporter ATP‑binding protein
* * ÷ NC_002947 5024709 5024794 86 4 [3] [3] 4 PP_4427 amino acid ABC transporter permease
* * ÷ NC_002947 5026993 5027084 92 5 [3] [3] 4 PP_4429 GntR family transcriptional regulator
* * ÷ NC_002947 5031573 5032006 434 4 [3] [3] 4 PP_4433 amino acid MFS transporter
* * ÷ NC_002947 5032020 5032179 160 4 [3] [2] 4 PP_4433 amino acid MFS transporter
* * ÷ NC_002947 5065498 5065698 201 4 [3] [3] 4 [PP_4460]–[PP_4461] [PP_4460],[PP_4461]
* * ÷ NC_002947 5101961 5101983 23 5 [0] [3] 4 PP_4488/phhR hypothetical protein/sigma‑54 dependent transcriptional regulator
* * ÷ NC_002947 5164559 5164576 18 4 [1] [3] 5 PP_4544/PP_4545 hypothetical protein/beta‑ketodecanoyl‑ACP synthase
* * ÷ NC_002947 5203578 5203615 38 4 [3] [1] 4 PP_4582/PP_4583 membrane protein/putative Peptidase
* * ÷ NC_002947 5346382 5346477 96 4 [3] [3] 4 [pgi‑II] [pgi‑II]
* * ÷ NC_002947 5487091 5487172 82 4 [3] [3] 4 purH/purD bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase/phosphoribosylamine‑‑glycine ligase
* * ÷ NC_002947 5508482 5508570 89 4 [3] [3] 4 [PP_4839] [PP_4839]
* * ÷ NC_002947 5540537 5540583 47 6 [3] [3] 4 PP_4871/PP_4872 lysine decarboxylase family protein/hypothetical protein
* * ÷ NC_002947 5657590 5657626 37 4 [3] [2] 6 epd/tktA D‑erythrose 4‑phosphate dehydrogenase/transketolase A
* * ÷ NC_002947 5818875 5818903 29 5 [2] [3] 4 PP_5092/pilT NLP/P60 protein/twitching motility protein
* * ÷ NC_002947 5899720 5899771 52 4 [3] [3] 4 PP_5172/PP_5173 hypothetical protein/RND family transporter
* * ÷ NC_002947 5905117 5905171 55 5 [3] [3] 4 PP_5175/PP_5176 HlyD family secretion protein/hypothetical protein
* * ÷ NC_002947 6082975 6082999 25 5 [3] [3] 4 [PP_5333] [PP_5333]
* * ÷ NC_002947 6165757 6165819 63 4 [2] [3] 4 PP_5405 transposase
* * ÷ NC_002947 6183852 6183858 7 20 [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)20 (0.620) 12/264 0.9 100% intergenic (–/+146) –/parB –/chromosome‑partitioning protein
?NC_002947 = 6183851 0 (0.000)intergenic (‑3/–) atpI/– ATP synthase protein I/–
* ? NC_002947 = 48101461 (0.030)10 (0.340) 5/240 1.9 35.1% intergenic (‑288/‑267) PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
?NC_002947 5990743 = 36 (1.230)intergenic (+59/‑487) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA