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 40,322 C→T 5.8% P81L (CCG→CTG)  fixA → predicted electron transfer flavoprotein subunit, ETFP adenine nucleotide‑binding domain
RA 89,548 A→G 13.6% E276G (GAA→GGA)  ftsA → ATP‑binding cell division protein involved in recruitment of FtsK to Z ring
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 55.5% D12A (GAT→GCT)  dnaQ → DNA polymerase III epsilon subunit
RA 214,931 A→C 59.3% E14A (GAA→GCA)  dnaQ → DNA polymerase III epsilon subunit
RA 317,968 C→T 13.7% T988T (ACC→ACT kefA → fused mechanosensitive channel proteins
RA 323,651 C→T 7.0% I21I (ATC→ATT htpG → molecular chaperone HSP90 family
RA 323,666 C→G 7.4% S26S (TCC→TCG htpG → molecular chaperone HSP90 family
RA 323,669 T→C 7.0% N27N (AAT→AAC htpG → molecular chaperone HSP90 family
RA 323,672 A→G 7.2% K28K (AAA→AAG htpG → molecular chaperone HSP90 family
RA 323,684 G→C 7.7% L32L (CTG→CTC htpG → molecular chaperone HSP90 family
RA 323,687 T→C 7.7% R33R (CGT→CGC htpG → molecular chaperone HSP90 family
RA 323,690 G→A 7.9% E34E (GAG→GAA htpG → molecular chaperone HSP90 family
RA 323,693 T→G 8.3% L35L (CTT→CTG htpG → molecular chaperone HSP90 family
RA 432,031:1 +T 6.7% coding (397/1407 nt) ybfM → predicted outer membrane porin
RA 894,873 C→T 5.5% E398K (GAA→AAA)  sapA ← predicted antimicrobial peptide transporter subunit
RA 936,986 G→A 7.0% G182G (GGG→GGA fdnI → formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible
RA 937,123 C→T 9.0% intergenic (+29/+378) fdnI → / ← yddM formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/predicted DNA‑binding transcriptional regulator
RA 974,093 A→G 7.4% T290A (ACG→GCG)  lsrB → AI2 transporter
RA 988,129 A→G 11.1% S790S (TCA→TCG ynfE → oxidoreductase subunit
RA 988,133 C→G 11.1% L792V (CTG→GTG)  ynfE → oxidoreductase subunit
RA 988,137 C→T 10.0% A793V (GCG→GTG)  ynfE → oxidoreductase subunit
RA 1,008,960 G→A 11.3% L98L (CTG→CTA folM → dihydrofolate reductase isozyme
RA 1,036,505 G→A 100% A632A (GCG→GCA rsxC → fused predicted 4Fe‑4S ferredoxin‑type protein
RA 1,141,208:1 +T 6.8% coding (168/264 nt) cedA ← cell division modulator
RA 1,213,226 A→G 10.0% *264R (TGA→CGA)  kdgR ← predicted DNA‑binding transcriptional regulator
RA 1,269,969 G→A 5.5% A74T (GCA→ACA)  yedP → conserved hypothetical protein
RA 1,440,761 C→G 9.2% intergenic (‑460/‑279) ompC ← / → rcsD outer membrane porin protein C/phosphotransfer intermediate protein in two‑component regulatory system with RcsBC
RA 1,440,764 C→G 8.8% intergenic (‑463/‑276) ompC ← / → rcsD outer membrane porin protein C/phosphotransfer intermediate protein in two‑component regulatory system with RcsBC
RA 1,477,381 A→G 9.2% E48G (GAA→GGA)  yfaH → conserved hypothetical protein
RA 1,642,784 T→A 10.0% P74P (CCA→CCT ypfJ ← conserved hypothetical protein
RA 1,642,808 T→C 15.6% Q66Q (CAA→CAG ypfJ ← conserved hypothetical protein
RA 1,682,955 G→A 8.6% R673R (CGC→CGT yfhM ← conserved hypothetical protein
RA 1,763,524 T→C 17.2% noncoding (320/1542 nt) rrsG ← 16S ribosomal RNA
RA 1,763,535 T→C 9.4% noncoding (309/1542 nt) rrsG ← 16S ribosomal RNA
RA 1,763,537 G→T 10.0% noncoding (307/1542 nt) rrsG ← 16S ribosomal RNA
RA 1,763,541 T→C 8.8% noncoding (303/1542 nt) rrsG ← 16S ribosomal RNA
RA 1,763,550 A→G 6.4% noncoding (294/1542 nt) rrsG ← 16S ribosomal RNA
RA 1,763,551 C→T 6.4% noncoding (293/1542 nt) rrsG ← 16S ribosomal RNA
RA 1,763,553 A→G 6.4% noncoding (291/1542 nt) rrsG ← 16S ribosomal RNA
RA 1,763,556 T→C 33.3% noncoding (288/1542 nt) rrsG ← 16S ribosomal RNA
RA 1,763,558 G→T 5.7% noncoding (286/1542 nt) rrsG ← 16S ribosomal RNA
RA 1,763,560 G→T 5.6% noncoding (284/1542 nt) rrsG ← 16S ribosomal RNA
RA 1,763,636 A→G 30.4% noncoding (208/1542 nt) rrsG ← 16S ribosomal RNA
RA 1,804,090 G→A 55.7% G52G (GGG→GGA mprA → DNA‑binding transcriptional regulator
RA 1,892,019:1 +GC 100% intergenic (‑437/+54) gudP ← / ← ygdL predicted D‑glucarate transporter/conserved hypothetical protein
RA 1,893,021 G→T 10.4% intergenic (‑142/+97) ygdL ← / ← mltA conserved hypothetical protein/membrane‑bound lytic murein transglycosylase A
RA 1,896,687 C→A 6.7% Q137K (CAG→AAG)  argA → fused acetylglutamate kinase homolog (inactive) and amino acid N‑acetyltransferase
RA 1,970,934 C→T 8.0% E658K (GAG→AAG)  speA ← biosynthetic arginine decarboxylase, PLP‑binding
RA 1,970,940 C→G 8.6% E656Q (GAA→CAA)  speA ← biosynthetic arginine decarboxylase, PLP‑binding
RA 2,065,298 T→C 7.7% D513D (GAT→GAC rpoD → RNA polymerase, sigma 70 (sigma D) factor
RA 2,065,301 T→C 7.7% D514D (GAT→GAC rpoD → RNA polymerase, sigma 70 (sigma D) factor
RA 2,065,304 A→C 7.1% E515D (GAA→GAC rpoD → RNA polymerase, sigma 70 (sigma D) factor
RA 2,108,696 A→T 5.1% D156V (GAT→GTT)  kbaY → tagatose 6‑phosphate aldolase 1, kbaY subunit
RA 2,262,864 G→A 10.6% S215S (TCC→TCT rplA ← 50S ribosomal subunit protein L1
RA 2,359,867 G→A 42.9% noncoding (1228/2905 nt) rrlA ← 23S ribosomal RNA
RA 2,359,876 C→T 34.5% noncoding (1219/2905 nt) rrlA ← 23S ribosomal RNA
RA 2,436,114 G→A 9.5% T608I (ACC→ATC)  rep ← DNA helicase and single‑stranded DNA‑dependent ATPase
RA 2,507,753 C→T 17.4% L273L (CTA→TTA)  yicI → predicted alpha‑glucosidase
RA 2,589,325 A→G 11.0% intergenic (‑1/+798) gadE ← / ← hdeD DNA‑binding transcriptional activator/acid‑resistance membrane protein
RA 2,676,291 G→T 5.5% V14F (GTT→TTT)  bioH → carboxylesterase of pimeloyl‑CoA synthesis
RA 2,859,245 G→T 8.0% D58Y (GAT→TAT)  mutL → methyl‑directed mismatch repair protein
RA 2,886,319 G→A 12.3% G191S (GGT→AGT)  ytfI → hypothetical protein
RA 2,948,260 G→A 7.8% intergenic (‑20/+118) yjjB ← / ← yjjP conserved inner membrane protein/predicted inner membrane protein
RA 2,982,587 T→C 11.8% G97G (GGT→GGC creB → DNA‑binding response regulator in two‑component regulatory system with CreC
RA 2,982,599 C→T 11.5% Y101Y (TAC→TAT creB → DNA‑binding response regulator in two‑component regulatory system with CreC

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? Exported = 706340 (0.650)16 (0.280)
+GATT
10/92 NT 42.0% coding (897/1431 nt) yaaJ predicted transporter
?Exported = 1611756 8 (0.130)coding (1397/1404 nt) eutA reactivating factor for ethanolamine ammonia lyase
* ? Exported 207434 =NA (NA)5 (0.090) 3/94 NT NA noncoding (2851/2904 nt) rrlH 23S ribosomal RNA
?Exported 207455 = NA (NA)noncoding (2872/2904 nt) rrlH 23S ribosomal RNA
* ? Exported = 21562246 (0.750)38 (1.350)
+27 bp
20/46 NT 62.3% coding (732/732 nt) dnaQ DNA polymerase III epsilon subunit
?Exported 2705182 = 54 (0.880)intergenic (+106/‑1) damX/dam hypothetical protein/DNA adenine methylase
* ? Exported 401088 =97 (1.580)5 (0.090) 3/88 NT 7.1% coding (448/1212 nt) dacA D‑alanyl‑D‑alanine carboxypeptidase
?Exported 401124 = 46 (0.850)coding (412/1212 nt) dacA D‑alanyl‑D‑alanine carboxypeptidase
* ? Exported 436259 =48 (0.780)66 (1.170) 29/92 NT 63.7% intergenic (‑156/‑29) ybfF/seqA conserved hypothetical protein/regulatory protein for replication initiation
?Exported = 2706018 31 (0.550)coding (836/837 nt) dam DNA adenine methylase
* ? Exported = 43683383 (1.360)107 (1.750) 41/100 NT 57.1% coding (546/546 nt) seqA regulatory protein for replication initiation
?Exported 1803907 = 78 (1.270)intergenic (+63/‑28) ygaH/mprA predicted inner membrane protein/DNA‑binding transcriptional regulator
* ? Exported = 60374034 (0.560)3 (0.070) 3/72 NT 9.2% intergenic (+22/‑188) ycaD/ycaM predicted transporter/predicted transporter
?Exported = 603748 35 (0.790)intergenic (+30/‑180) ycaD/ycaM predicted transporter/predicted transporter
* ? Exported 1334516 =56 (0.910)7 (0.110) 3/100 NT 10.0% coding (313/480 nt) nudD GDP‑mannose mannosyl hydrolase
?Exported 1334537 = 70 (1.140)coding (292/480 nt) nudD GDP‑mannose mannosyl hydrolase
* ? Exported = 153767173 (1.190)9 (0.170) 3/88 NT 10.7% coding (834/897 nt) yfcT predicted outer membrane export usher protein
?Exported = 1537689 86 (1.600)coding (816/897 nt) yfcT predicted outer membrane export usher protein
* ? Exported 1611749 =5 (0.080)23 (0.440)
+ATGCGGT
12/86 NT 49.8% coding (1404/1404 nt) eutA reactivating factor for ethanolamine ammonia lyase
?Exported = 2603083 49 (0.800)coding (684/753 nt) yhiQ predicted SAM‑dependent methyltransferase
* ? Exported 2267011 =89 (1.450)5 (0.090) 3/90 NT 7.3% intergenic (‑12/‑350) thrU/coaA tRNA‑Thr/pantothenate kinase
?Exported 2267032 = 46 (0.840)intergenic (‑33/‑329) thrU/coaA tRNA‑Thr/pantothenate kinase
* ? Exported 2749095 =70 (1.140)7 (0.130) 3/90 NT 10.2% coding (1168/1332 nt) secY preprotein translocase membrane subunit
?Exported 2749115 = 60 (1.090)coding (1188/1332 nt) secY preprotein translocase membrane subunit