breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation freq annotation gene description
RA 13,583 T→G 6.6% V474G (GTT→GGT)  dnaK → chaperone Hsp70, co‑chaperone with DnaJ
RA 13,586 C→A 6.5% T475N (ACC→AAC)  dnaK → chaperone Hsp70, co‑chaperone with DnaJ
RA 13,594 A→C 6.1% I478L (ATC→CTC)  dnaK → chaperone Hsp70, co‑chaperone with DnaJ
RA 62,466 A→G 5.1% Y331Y (TAT→TAC polB ← DNA polymerase II
RA 62,471 T→A 5.2% T330S (ACT→TCT)  polB ← DNA polymerase II
RA 62,472 T→G 5.2% A329A (GCA→GCC polB ← DNA polymerase II
RA 62,484 T→C 5.3% K325K (AAA→AAG polB ← DNA polymerase II
RA 72,621 A→G 7.1% intergenic (+33/‑147) ilvH → / → fruR acetolactate synthase III, thiamin‑dependent, small subunit/DNA‑binding transcriptional dual regulator
RA 72,624 T→A 7.2% intergenic (+36/‑144) ilvH → / → fruR acetolactate synthase III, thiamin‑dependent, small subunit/DNA‑binding transcriptional dual regulator
RA 72,627 C→T 7.4% intergenic (+39/‑141) ilvH → / → fruR acetolactate synthase III, thiamin‑dependent, small subunit/DNA‑binding transcriptional dual regulator
RA 129,042 C→T 9.4% L201L (CTG→TTG)  yadH → predicted transporter subunit
RA 204,511 C→T 100% intergenic (+111/‑73) alaV → / → rrlH tRNA‑Ala/23S ribosomal RNA
RA 204,556 A→G 100% intergenic (+156/‑28) alaV → / → rrlH tRNA‑Ala/23S ribosomal RNA
RA 214,925 A→C 56.9% D12A (GAT→GCT)  dnaQ → DNA polymerase III epsilon subunit
RA 214,931 A→C 57.1% E14A (GAA→GCA)  dnaQ → DNA polymerase III epsilon subunit
RA 225,827 T→C 8.2% intergenic (+14/‑78) gpt → / → frsA guanine‑hypoxanthine phosphoribosyltransferase/hydrolase, binds to enzyme IIA(Glc)
RA 266,222 C→T 6.7% R128H (CGC→CAC)  yajO ← predicted oxidoreductase, NAD(P)‑binding
RA 1,028,431 C→T 8.7% A462A (GCC→GCT malX → fused maltose and glucose‑specific PTS enzyme IIBC components
RA 1,036,505 G→A 100% A632A (GCG→GCA rsxC → fused predicted 4Fe‑4S ferredoxin‑type protein
RA 1,262,097 A→T 7.8% intergenic (‑49/+339) torY ← / ← cutC TMAO reductase III (TorYZ), cytochrome c‑type subunit/copper homeostasis protein
RA 1,363,919 G→T 5.4% R470L (CGC→CTC)  metG → methionyl‑tRNA synthetase
RA 1,364,064 A→G 5.9% Q518Q (CAA→CAG metG → methionyl‑tRNA synthetase
RA 1,364,066 C→G 5.9% P519R (CCG→CGG)  metG → methionyl‑tRNA synthetase
RA 1,364,068 C→T 7.2% L520L (CTG→TTG)  metG → methionyl‑tRNA synthetase
RA 1,421,797 C→T 7.4% T220T (ACG→ACA ccmF ← heme lyase, CcmF subunit
RA 1,746,320 G→A 5.7% E247K (GAA→AAA)  srmB → ATP‑dependent RNA helicase
RA 1,763,556 T→C 44.3% noncoding (288/1542 nt) rrsG ← 16S ribosomal RNA
RA 1,763,558 G→C 6.9% noncoding (286/1542 nt) rrsG ← 16S ribosomal RNA
RA 1,763,636 A→G 17.3% noncoding (208/1542 nt) rrsG ← 16S ribosomal RNA
RA 1,804,090 G→A 49.3% G52G (GGG→GGA mprA → DNA‑binding transcriptional regulator
RA 1,814,931 A→G 7.2% G82G (GGT→GGC alaS ← alanyl‑tRNA synthetase
RA 1,814,958 A→G 5.1% G73G (GGT→GGC alaS ← alanyl‑tRNA synthetase
RA 1,814,961 A→G 5.1% G72G (GGT→GGC alaS ← alanyl‑tRNA synthetase
RA 1,814,964 C→G 5.1% A71A (GCG→GCC alaS ← alanyl‑tRNA synthetase
RA 1,814,967 A→G 5.0% R70R (CGT→CGC alaS ← alanyl‑tRNA synthetase
RA 1,892,019:1 +GC 100% intergenic (‑437/+54) gudP ← / ← ygdL predicted D‑glucarate transporter/conserved hypothetical protein
RA 2,064,071 A→G 6.1% E104E (GAA→GAG rpoD → RNA polymerase, sigma 70 (sigma D) factor
RA 2,064,080 C→G 6.5% T107T (ACC→ACG rpoD → RNA polymerase, sigma 70 (sigma D) factor
RA 2,064,086 A→G 5.2% E109E (GAA→GAG rpoD → RNA polymerase, sigma 70 (sigma D) factor
RA 2,064,095 C→G 5.3% T112T (ACC→ACG rpoD → RNA polymerase, sigma 70 (sigma D) factor
RA 2,065,001 A→G 5.5% K414K (AAA→AAG rpoD → RNA polymerase, sigma 70 (sigma D) factor
RA 2,065,007 T→G 5.7% V416V (GTT→GTG rpoD → RNA polymerase, sigma 70 (sigma D) factor
RA 2,065,010 T→C 5.4% D417D (GAT→GAC rpoD → RNA polymerase, sigma 70 (sigma D) factor
RA 2,065,013 A→G 6.0% K418K (AAA→AAG rpoD → RNA polymerase, sigma 70 (sigma D) factor
RA 2,068,683 G→C 7.8% A369A (GCC→GCG aer ← fused signal transducer for aerotaxis sensory component and methyl accepting chemotaxis component
RA 2,068,689 A→G 6.5% I367I (ATT→ATC aer ← fused signal transducer for aerotaxis sensory component and methyl accepting chemotaxis component
RA 2,086,490 C→A 5.8% P89T (CCG→ACG)  yqjG → predicted S‑transferase
RA 2,139,798 T→C 11.1% N437S (AAC→AGC)  infB ← fused protein chain initiation factor 2, IF2
RA 2,139,800 T→C 11.1% E436E (GAA→GAG) ‡ infB ← fused protein chain initiation factor 2, IF2
RA 2,139,801 T→G 11.1% E436A (GAA→GCA) ‡ infB ← fused protein chain initiation factor 2, IF2
RA 2,139,802 C→G 10.4% E436Q (GAA→CAA) ‡ infB ← fused protein chain initiation factor 2, IF2
RA 2,139,803 A→G 10.5% T435T (ACT→ACC infB ← fused protein chain initiation factor 2, IF2
RA 2,139,806 T→G 11.1% E434D (GAA→GAC infB ← fused protein chain initiation factor 2, IF2
RA 2,139,809 A→C 10.3% V433V (GTT→GTG infB ← fused protein chain initiation factor 2, IF2
RA 2,139,824 A→G 14.4% I428I (ATT→ATC infB ← fused protein chain initiation factor 2, IF2
RA 2,257,303 T→C 6.7% A1280A (GCA→GCG rpoB ← RNA polymerase, beta subunit
RA 2,266,165 G→A 7.8% I93I (ATC→ATT tufB ← protein chain elongation factor EF‑Tu
RA 2,266,174 T→C 9.4% K90K (AAA→AAG tufB ← protein chain elongation factor EF‑Tu
RA 2,266,177 A→G 9.6% V89V (GTT→GTC) ‡ tufB ← protein chain elongation factor EF‑Tu
RA 2,266,179 C→T 9.6% V89I (GTT→ATT) ‡ tufB ← protein chain elongation factor EF‑Tu
RA 2,266,180 A→G 9.6% Y88Y (TAT→TAC tufB ← protein chain elongation factor EF‑Tu
RA 2,359,867 G→A 52.9% noncoding (1228/2905 nt) rrlA ← 23S ribosomal RNA
RA 2,359,876 C→T 51.0% noncoding (1219/2905 nt) rrlA ← 23S ribosomal RNA
RA 2,398,822 T→G 6.0% V603V (GTA→GTC uvrD ← DNA‑dependent ATPase I and helicase II
RA 2,398,828 A→G 5.2% V601V (GTT→GTC uvrD ← DNA‑dependent ATPase I and helicase II
RA 2,432,727 A→G 5.2% I42I (ATT→ATC trxA ← thioredoxin 1
RA 2,432,736 G→A 5.3% I39I (ATC→ATT trxA ← thioredoxin 1
RA 2,432,742 T→C 5.5% K37K (AAA→AAG trxA ← thioredoxin 1
RA 2,469,756 T→C 5.1% Y246Y (TAT→TAC atpD → F1 sector of membrane‑bound ATP synthase, beta subunit
RA 2,494,963 C→T 7.4% intergenic (+17/‑125) ibpB → / → yidF heat shock chaperone/predicted DNA‑binding transcriptional regulator
RA 2,638,449 C→T 8.4% R147R (CGC→CGT ugpC → glycerol‑3‑phosphate transporter subunit
RA 2,638,461 C→T 6.8% R151R (CGC→CGT ugpC → glycerol‑3‑phosphate transporter subunit
RA 2,736,245 A→G 5.4% E463E (GAA→GAG fusA → protein chain elongation factor EF‑G
RA 2,736,254 C→G 5.1% L466L (CTC→CTG fusA → protein chain elongation factor EF‑G
RA 2,736,257 C→A 5.3% D467E (GAC→GAA fusA → protein chain elongation factor EF‑G
RA 2,736,260 C→T 5.5% I468I (ATC→ATT fusA → protein chain elongation factor EF‑G
RA 2,736,272 T→C 5.0% R472R (CGT→CGC fusA → protein chain elongation factor EF‑G
RA 2,770,171 G→A 7.8% V232M (GTG→ATG)  metA → homoserine transsuccinylase
RA 2,802,251 A→G 11.0% S285S (TCT→TCC qor ← quinone oxidoreductase, NADPH‑dependent
RA 2,810,841 A→C 15.2% F635L (TTT→TTG) ‡ uvrA ← ATPase and DNA damage recognition protein of nucleotide excision repair excinuclease UvrABC
RA 2,810,843 A→T 15.2% F635I (TTT→ATT) ‡ uvrA ← ATPase and DNA damage recognition protein of nucleotide excision repair excinuclease UvrABC
RA 2,810,847 A→G 16.2% G633G (GGT→GGC uvrA ← ATPase and DNA damage recognition protein of nucleotide excision repair excinuclease UvrABC
RA 2,810,858 G→A 15.9% L630L (CTG→TTG)  uvrA ← ATPase and DNA damage recognition protein of nucleotide excision repair excinuclease UvrABC
RA 2,810,859 C→G 15.9% T629T (ACG→ACC uvrA ← ATPase and DNA damage recognition protein of nucleotide excision repair excinuclease UvrABC
RA 2,810,865 C→G 15.9% T627T (ACG→ACC uvrA ← ATPase and DNA damage recognition protein of nucleotide excision repair excinuclease UvrABC
RA 2,810,871 G→A 11.1% D625D (GAC→GAT uvrA ← ATPase and DNA damage recognition protein of nucleotide excision repair excinuclease UvrABC
RA 2,827,243 G→C 8.4% T336S (ACT→AGT)  dcuA ← C4‑dicarboxylate antiporter
RA 2,937,896 C→T 5.1% intergenic (+23/‑246) leuX → / → yjhV tRNA‑Leu/hypothetical protein

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? minE = 7063105 (0.990)26 (0.270)
+GATT
7/90 NT 32.7% coding (897/1431 nt) yaaJ predicted transporter
?minE = 1611756 12 (0.110)coding (1397/1404 nt) eutA reactivating factor for ethanolamine ammonia lyase
* ? minE 62035 =66 (0.620)8 (0.080) 3/90 NT 9.9% coding (1424/2352 nt) polB DNA polymerase II
?minE 62063 = 85 (0.870)coding (1396/2352 nt) polB DNA polymerase II
* ? minE 89211 =195 (1.840)13 (0.140) 3/84 NT 8.1% coding (490/1263 nt) ftsA ATP‑binding cell division protein involved in recruitment of FtsK to Z ring
?minE 89257 = 129 (1.420)coding (536/1263 nt) ftsA ATP‑binding cell division protein involved in recruitment of FtsK to Z ring
* ? minE = 203035NA (NA)5 (0.050) 3/92 NT NA noncoding (440/1542 nt) rrsH 16S ribosomal RNA
?minE = 203088 NA (NA)noncoding (493/1542 nt) rrsH 16S ribosomal RNA
* ? minE = 203909NA (NA)5 (0.060) 3/84 NT NA noncoding (1314/1542 nt) rrsH 16S ribosomal RNA
?minE = 203917 NA (NA)noncoding (1322/1542 nt) rrsH 16S ribosomal RNA
* ? minE = 204740NA (NA)17 (0.190) 5/82 NT NA noncoding (157/2904 nt) rrlH 23S ribosomal RNA
?minE = 204751 NA (NA)noncoding (168/2904 nt) rrlH 23S ribosomal RNA
* ? minE = 206767NA (NA)15 (0.150) 4/94 NT NA noncoding (2184/2904 nt) rrlH 23S ribosomal RNA
?minE = 206784 NA (NA)noncoding (2201/2904 nt) rrlH 23S ribosomal RNA
* ? minE = 21562248 (0.450)58 (1.250)
+27 bp
23/44 NT 68.7% coding (732/732 nt) dnaQ DNA polymerase III epsilon subunit
?minE 2705182 = 73 (0.690)intergenic (+106/‑1) damX/dam hypothetical protein/DNA adenine methylase
* ? minE = 328743124 (1.170)6 (0.060) 3/90 NT 6.2% coding (150/1305 nt) gsk inosine/guanosine kinase
?minE = 328786 67 (0.690)coding (193/1305 nt) gsk inosine/guanosine kinase
* ? minE = 344913107 (1.010)14 (0.160) 3/82 NT 11.4% coding (526/678 nt) ybbL predicted transporter subunit
?minE = 344930 128 (1.450)coding (543/678 nt) ybbL predicted transporter subunit
* ? minE 436259 =83 (0.780)76 (0.780) 35/90 NT 57.1% intergenic (‑156/‑29) ybfF/seqA conserved hypothetical protein/regulatory protein for replication initiation
?minE = 2706018 38 (0.390)coding (836/837 nt) dam DNA adenine methylase
* ? minE = 436833114 (1.070)150 (1.410) 39/98 NT 57.1% coding (546/546 nt) seqA regulatory protein for replication initiation
?minE 1803907 = 111 (1.040)intergenic (+63/‑28) ygaH/mprA predicted inner membrane protein/DNA‑binding transcriptional regulator
* ? minE 566067 =141 (1.330)12 (0.130) 3/86 NT 10.2% coding (1682/1719 nt) poxB pyruvate dehydrogenase (pyruvate oxidase), thiamin‑dependent, FAD‑binding
?minE 566089 = 87 (0.940)coding (1660/1719 nt) poxB pyruvate dehydrogenase (pyruvate oxidase), thiamin‑dependent, FAD‑binding
* ? minE = 115254679 (0.740)11 (0.120) 3/82 NT 10.4% coding (83/576 nt) ydjR conserved hypothetical protein
?minE = 1152570 123 (1.390)coding (59/576 nt) ydjR conserved hypothetical protein
* ? minE 1669623 =61 (0.570)8 (0.090) 3/86 NT 13.7% coding (420/1473 nt) der predicted GTP‑binding protein
?minE 1669653 = 47 (0.510)coding (390/1473 nt) der predicted GTP‑binding protein
* ? minE 1994733 =75 (0.710)9 (0.090) 3/88 NT 12.6% coding (1417/2136 nt) speC ornithine decarboxylase, constitutive
?minE 1994757 = 58 (0.610)coding (1393/2136 nt) speC ornithine decarboxylase, constitutive
* ? minE 2159817 =34 (0.320)6 (0.070) 3/84 NT 10.2% intergenic (+43/‑185) ispB/sfsB octaprenyl diphosphate synthase/DNA‑binding transcriptional regulator
?minE 2159914 = 77 (0.850)intergenic (+140/‑88) ispB/sfsB octaprenyl diphosphate synthase/DNA‑binding transcriptional regulator
* ? minE 2356934 =119 (1.120)8 (0.080) 3/88 NT 7.4% coding (321/585 nt) mobA molybdopterin‑guanine dinucleotide synthase
?minE 2356958 = 93 (0.980)coding (345/585 nt) mobA molybdopterin‑guanine dinucleotide synthase
* ? minE 2816800 =72 (0.680)4 (0.040) 3/86 NT 6.0% intergenic (+17/‑80) soxR/nrfA DNA‑binding transcriptional dual regulator, Fe‑S center for redox‑sensing/nitrite reductase, formate‑dependent, cytochrome
?minE 2816824 = 62 (0.670)intergenic (+41/‑56) soxR/nrfA DNA‑binding transcriptional dual regulator, Fe‑S center for redox‑sensing/nitrite reductase, formate‑dependent, cytochrome
* ? minE = 2928756138 (1.300)11 (0.120) 3/88 NT 7.4% coding (55/1083 nt) yjgQ conserved inner membrane protein
?minE = 2928777 150 (1.580)coding (76/1083 nt) yjgQ conserved inner membrane protein