mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 7,192 | Δ1 bp | coding (768/1431 nt) | yaaJ ← | putative transporter YaaJ |
| RA | 59,029 | C→T | P186S (CCT→TCT) | yabP → | putative uncharacterized protein YabP |
| RA | 70,787 | T→C | F134S (TTT→TCT) | araC → | DNA‑binding transcriptional dual regulator AraC |
| RA | 106,321 | C→T | Y339Y (TAC→TAT) | ftsZ → | cell division protein FtsZ |
| RA | 135,657 | T→C | T270A (ACG→GCG) | speE ← | spermidine synthase |
| RA | 163,050 | T→C | S316P (TCC→CCC) | hrpB → | putative ATP‑dependent RNA helicase HrpB |
| RA | 170,165 | G→A | E130K (GAA→AAA) | fhuC → | iron(III) hydroxamate ABC transporter ATP binding subunit |
| RA | 176,052 | G→A | G316S (GGT→AGT) | clcA → | chloride:H(+) antiporter ClcA |
| RA | 241,471 | (C)5→6 | coding (1833/2445 nt) | fadE ← | acyl‑CoA dehydrogenase |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 478,313 | A→G | V102A (GTT→GCT) | pdeB ← | c‑di‑GMP phosphodiesterase PdeB |
| RA | 511,054 | C→T | S109N (AGC→AAC) | copA ← | Cu(+) exporting P‑type ATPase |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 577,732 | A→G | I40M (ATA→ATG) | rrrD → | DLP12 prophage; lysozyme |
| RA | 587,227 | C→T | G252D (GGC→GAC) | ybcH ← | DUF4434 domain‑containing protein YbcH |
| RA | 809,295 | A→G | intergenic (‑38/‑49) | bioA ← / → bioB | adenosylmethionine‑8‑amino‑7‑oxononanoate aminotransferase/biotin synthase |
| RA | 827,858 | A→G | M375T (ATG→ACG) | ybhF ← | putative ABC exporter ATP binding subunit |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,041,989 | A→G | intergenic (+74/+41) | appA → / ← etk | periplasmic phosphoanhydride phosphatase/multiple inositol‑polyphosphate phosphatase/protein‑tyrosine kinase Etk |
| RA | 1,073,603 | T→C | T137A (ACT→GCT) | rutA ← | pyrimidine oxygenase |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,159,521 | C→T | A677A (GCG→GCA) | fhuE ← | ferric coprogen/ferric rhodotorulic acid outer membrane transporter |
| RA | 1,185,889 | A→G | T16A (ACC→GCC) | pepT → | peptidase T |
| RA | 1,211,898 | Δ1 bp | coding (106/324 nt) | iraM ← | anti‑adaptor protein IraM, inhibitor of sigma(S) proteolysis |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,242,448 | A→G | R211R (CGT→CGC) | ldcA ← | murein L,D‑carboxypeptidase |
| RA | 1,244,821 | A→G | T32A (ACC→GCC) | ymgE → | PF04226 family protein YmgE |
| RA | 1,311,875 | T→C | G124G (GGA→GGG) | yciA ← | acyl‑CoA thioesterase |
| RA | 1,318,580 | A→G | V403V (GTT→GTC) | trpC ← | fused indole‑3‑glycerol phosphate synthase/phosphoribosylanthranilate isomerase |
| RA | 1,320,484 | C→T | G301R (GGG→AGG) | trpD ← | anthranilate synthase subunit TrpD |
| RA | 1,370,044 | (T)9→8 | intergenic (+41/‑172) | pspE → / → ycjM | thiosulfate sulfurtransferase PspE/glucosylglycerate phosphorylase |
| RA | 1,412,779 | (T)6→5 | coding (457/1236 nt) | intR ← | Rac prophage; putative integrase |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,548,132 | G→A | A244A (GCG→GCA) | fdnG → | formate dehydrogenase N subunit alpha |
| RA | 1,566,914 | A→G | V76A (GTG→GCG) | dosC ← | diguanylate cyclase DosC |
| RA | 1,570,763 | C→T | G428D (GGC→GAC) | gadB ← | glutamate decarboxylase B |
| RA | 1,594,256 | (C)8→9 | pseudogene (3831/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,597,095 | A→G | pseudogene (992/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,681,103 | C→T | A43V (GCC→GTC) | folM → | dihydromonapterin reductase |
| RA | 1,683,057 | (C)6→7 | coding (176/1302 nt) | rstB → | sensory histidine kinase RstB |
| RA | 1,684,783 | A→G | K175K (AAA→AAG) | tus → | DNA replication terminus site‑binding protein |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,705,838 | T→C | G24G (GGT→GGC) | rsxA → | SoxR [2Fe‑2S] reducing system protein RsxA |
| RA | 1,717,500 | C→T | G170S (GGC→AGC) | pdxH ← | pyridoxal 5‑phosphate synthase |
| RA | 1,727,492 | G→A | G278G (GGG→GGA) | nemA → | N‑ethylmaleimide reductase |
| RA | 1,744,504 | G→A | V350I (GTT→ATT) | mdtK → | multidrug efflux pump MdtK |
| RA | 1,784,524 | (T)7→6 | coding (1548/1701 nt) | fadK → | short chain acyl‑CoA synthetase |
| RA | 1,852,745 | T→C | H412R (CAT→CGT) | ydjE ← | putative transporter YdjE |
| RA | 1,873,384 | A→G | K448K (AAA→AAG) | dgcJ → | putative diguanylate cyclase DgcJ |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,903,984 | T→C | G30G (GGT→GGC) | manZ → | mannose‑specific PTS enzyme IID component |
| RA | 1,909,423 | A→G | I226T (ATC→ACC) | kdgR ← | DNA‑binding transcriptional repressor KdgR |
| RA | 1,950,998 | T→C | V56A (GTT→GCT) | yecD → | putative hydrolase |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 1,990,223 | G→A | G181G (GGG→GGA) | tyrP → | tyrosine:H(+) symporter |
| RA | 1,996,183 | T→C | N217S (AAC→AGC) | sdiA ← | DNA‑binding transcriptional dual regulator SdiA |
| RA | 2,003,907 | T→C | G12G (GGT→GGC) | fliD → | flagellar filament capping protein |
| RA | 2,009,605 | T→C | C43R (TGT→CGT) | yedF → | putative sulfurtransferase YedF |
| RA | 2,016,495 | G→A | A210T (GCC→ACC) | fliH → | flagellar biosynthesis protein FliH |
| RA | 2,024,266 | (A)6→5 | coding (299/624 nt) | rcsA → | DNA‑binding transcriptional activator RcsA |
| RA | 2,072,123 | A→G | G195G (GGA→GGG) | flu → | CP4‑44 prophage; self recognizing antigen 43 (Ag43) autotransporter |
| RA | 2,088,388 | A→G | G247G (GGT→GGC) | yeeZ ← | putative epimerase YeeZ |
| RA | 2,097,752 | T→C | T184A (ACG→GCG) | wzzB ← | regulator of length of O‑antigen component of lipopolysaccharide chains |
| RA | 2,119,684 | T→C | T159A (ACG→GCG) | wzxC ← | M‑antigen undecaprenyl disphosphate flippase |
| RA | 2,165,573 | (C)6→7 | intergenic (+52/‑95) | yegP → / → yegQ | DUF1508 domain‑containing protein YegP/putative peptidase YegQ |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,228,558 | T→C | pseudogene (201/1436 nt) | mdtQ ← | putative multidrug resistance outer membrane protein MdtQ |
| RA | 2,253,116 | T→C | T344A (ACG→GCG) | nupX ← | putative nucleoside transporter |
| RA | 2,294,012 | A→G | V298A (GTG→GCG) | ccmF ← | holocytochrome c synthetase membrane subunit CcmF |
| RA | 2,306,567 | T→C | E63G (GAG→GGG) | mqo ← | malate:quinone oxidoreductase |
| RA | 2,319,804 | G→A | L25F (CTC→TTC) | rcsC ← | sensory histidine kinase RcsC |
| RA | 2,339,161 | T→C | D87G (GAC→GGC) | gyrA ← | DNA gyrase subunit A |
| RA | 2,355,297 | T→C | Y345H (TAT→CAT) | glpB → | anaerobic glycerol‑3‑phosphate dehydrogenase subunit B |
| RA | 2,356,131 | T→C | V204A (GTA→GCA) | glpC → | anaerobic glycerol‑3‑phosphate dehydrogenase subunit C |
| RA | 2,389,499 | A→G | E128E (GAA→GAG) | yfbP → | uncharacterized protein YfbP |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,503,270 | T→C | T406A (ACC→GCC) | fryA ← | putative PTS multiphosphoryl transfer protein FryA |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,565,722 | A→G | V388A (GTC→GCC) | eutA ← | reactivating factor for ethanolamine ammonia‑lyase EutBC |
| RA | 2,740,658 | C→T | A165T (GCT→ACT) | aroF ← | 3‑deoxy‑7‑phosphoheptulonate synthase, Tyr‑sensitive |
| RA | 2,762,824 | T→C | K239K (AAA→AAG) | abpB ← | CP4‑57 prophage; putative helicase YfjK |
| RA | 2,770,794 | G→A | T38T (ACG→ACA) | yfjS → | CP4‑57 prophage; inner membrane lipoprotein YfjS |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,940,965 | T→C | L93L (TTA→TTG) | rlmM ← | 23S rRNA 2'‑O‑ribose C2498 methyltransferase |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,952,313 | T→C | H50R (CAC→CGC) | recD ← | exodeoxyribonuclease V subunit RecD |
| RA | 2,967,224 | T→C | E404G (GAA→GGA) | ptsP ← | phosphoenolpyruvate‑protein phosphotransferase PtsP |
| RA | 3,060,960 | G→A | P37P (CCG→CCA) | scpA → | methylmalonyl‑CoA mutase |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,078,994 | C→T | G113S (GGC→AGC) | cmtB ← | mannitol‑specific PTS enzyme IIA component CmtB |
| RA | 3,079,957 | T→C | E560G (GAA→GGA) | tktA ← | transketolase 1 |
| RA | 3,101,039 | (C)7→8 | coding (585/720 nt) | yggN ← | putative EcfF |
| RA | 3,128,145 | (T)8→7 | intergenic (‑124/‑127) | glcD ← / → glcC | glycolate dehydrogenase, putative FAD‑linked subunit/DNA‑binding transcriptional dual regulator GlcC |
| RA | 3,164,107 | T→C | T623A (ACC→GCC) | parC ← | DNA topoisomerase IV subunit A |
| RA | 3,240,984 | (G)7→8 | coding (1041/1245 nt) | sstT → | serine/threonine:Na(+) symporter |
| RA | 3,269,142 | A→G | D243G (GAC→GGC) | yhaC → | uncharacterized protein YhaC |
| RA | 3,282,504 | A→G | T177A (ACC→GCC) | agaS → | putative galactosamine‑6‑phosphate deaminase/isomerase |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,390,414 | T→C | F299L (TTT→CTT) | aaeR → | LysR‑type transcriptional regulator AaeR |
| RA | 3,401,710 | T→C | V541V (GTA→GTG) | csrD ← | regulator of CsrB and CsrC decay |
| RA | 3,428,918 | Δ1 bp | intergenic (‑156/‑318) | rrsD ← / → yrdA | 16S ribosomal RNA/protein YrdA |
| RA | 3,428,923 | Δ1 bp | intergenic (‑161/‑313) | rrsD ← / → yrdA | 16S ribosomal RNA/protein YrdA |
| RA | 3,428,927 | T→G | intergenic (‑165/‑309) | rrsD ← / → yrdA | 16S ribosomal RNA/protein YrdA |
| RA | 3,481,078 | T→C | K28K (AAA→AAG) | kefG ← | protein required for KefB activity |
| RA | 3,551,477 | C→T | A333T (GCC→ACC) | malP ← | maltodextrin phosphorylase |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,660,928 | T→C | V172A (GTT→GCT) | mdtF → | multidrug efflux pump RND permease MdtF |
| RA | 3,743,076 | A→G | N115S (AAC→AGC) | yiaK → | 2,3‑diketo‑L‑gulonate reductase |
| RA | 3,812,130 | T→C | T144A (ACG→GCG) | yicR ← | RadC‑like JAB domain‑containing protein YicR |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,931,183 | (G)7→6 | intergenic (‑90/‑133) | ravA ← / → kup | regulatory ATPase RavA/K(+):H(+) symporter Kup |
| RA | 3,965,878 | G→A | A40T (GCC→ACC) | trxA → | thioredoxin 1 |
| RA | 4,201,683 | T→C | K2K (AAA→AAG) | zraP ← | zinc responsive, periplasmic protein with chaperone activity |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,358,768 | A→G | F422L (TTC→CTC) | cadB ← | lysine:cadaverine antiporter |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,495,235 | G→A | R325R (CGC→CGT) | ahr ← | aldehyde reductase, NADPH‑dependent |
| RA | 4,532,980 | A→G | S68S (AGT→AGC) | yjhP ← | KpLE2 phage‑like element; putative methyltransferase YjhP |
| RA | 4,539,902 | T→C | intergenic (‑401/‑1055) | nanC ← / → fimB | N‑acetylneuraminic acid outer membrane channel/regulator for fimA |
| RA | 4,606,094 | (G)8→9 | noncoding (72/87 nt) | leuV ← | tRNA‑Leu |
| RA | 4,629,992 | C→T | L177L (CTG→CTA) | ettA ← | energy‑dependent translational throttle protein EttA |
| RA | 4,631,420 | A→G | T230A (ACC→GCC) | slt → | soluble lytic murein transglycosylase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423770–3424233 | 3424523–3424238 | 6–754 | 21 [16] | [13] 21 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3762349–3764072 | 3765176–3764078 | 7–2828 | 19 [17] | [15] 18 | rhsA | rhs element protein RhsA |
| * | * | ÷ | NC_000913 | 4038847–4039385 | 4040515–4039392 | 8–1669 | 18 [17] | [17] 18 | [rrlA] | [rrlA] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 374921 = | NA (NA) | 40 (0.790) | 12/190 | 2.4 | NA | intergenic (+40/‑538) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377531 = | NA (NA) | intergenic (+220/+4) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 50 (0.980) | 19/190 | 1.3 | NA | noncoding (33/34 nt) | other | REP31a |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 1207805 | 74 (1.000) | 17 (0.260) | 15/244 | 2.6 | 21.6% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 58 (0.890) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 82 (1.140) | 52/268 | 0.2 | 100% | intergenic (+253/‑33) | ychE/insH21 | putative inner membrane protein/IS5 transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 3363001 = | 105 (1.420) | 109 (1.480) | 63/274 | 0.1 | 67.7% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 0 (0.000) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 89 (1.200) | 51/276 | 0.3 | 97.8% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 2 (0.030) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||