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 | 13,217 | A→G | K352R (AAA→AGA) | dnaK → | chaperone protein DnaK |
| RA | 23,734 | C→T | G448G (GGC→GGT) | ileS → | isoleucine‑‑tRNA ligase |
| RA | 27,745 | T→C | G151G (GGT→GGC) | rihC → | ribonucleoside hydrolase RihC |
| RA | 99,352 | T→C | L317S (TTA→TCA) | ftsW → | putative lipid II flippase FtsW |
| RA | 237,555 | A→G | E74G (GAG→GGG) | yafT → | lipoprotein YafT |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 260,321 | A→G | intergenic (‑221/‑67) | phoE ← / → proB | outer membrane porin PhoE/glutamate 5‑kinase |
| RA | 308,290 | A→G | V348A (GTC→GCC) | ecpC ← | putative fimbrial usher protein EcpC |
| RA | 308,579 | A→G | S252P (TCC→CCC) | ecpC ← | putative fimbrial usher protein EcpC |
| RA | 331,290 | G→A | G610S (GGC→AGC) | betT → | choline:H(+) symporter |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 399,795 | A→G | N68S (AAC→AGC) | yaiZ → | DUF2754 domain‑containing protein YaiZ |
| RA | 410,250 | A→G | Y36C (TAC→TGC) | mak → | manno(fructo)kinase |
| RA | 420,584 | G→A | G332S (GGC→AGC) | brnQ → | branched chain amino acid transporter BrnQ |
| RA | 432,938 | C→T | intergenic (‑87/‑64) | yajI ← / → nrdR | putative lipoprotein YajI/NrdR transcriptional repressor |
| RA | 476,575 | A→G | intergenic (+14/‑97) | ffs → / → ybaA | signal recognition particle 4.5S RNA/DUF1428 domain‑containing protein YbaA |
| RA | 485,731 | T→C | intergenic (‑112/‑30) | acrA ← / → acrR | multidrug efflux pump membrane fusion lipoprotein AcrA/DNA‑binding transcriptional repressor AcrR |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 528,946 | C→A | pseudogene (307/491 nt) | ybbD → | putative uncharacterized protein YbbD |
| RA | 708,162 | C→T | intergenic (+405/‑172) | glnS → / → chiP | glutamine‑‑tRNA ligase/chitobiose outer membrane channel |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 907,292 | T→C | T331A (ACC→GCC) | ybjT ← | putative NAD(P)‑dependent oxidoreductase YbjT |
| 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 | 1,020,878 | T→C | S14S (TCA→TCG) | sulA ← | cell division inhibitor SulA |
| RA | 1,112,249 | (G)6→7 | coding (1387/2544 nt) | opgH → | osmoregulated periplasmic glucans (OPGs) biosynthesis protein H |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,164,005 | A→G | Y249C (TAC→TGC) | thiK → | thiamine kinase |
| RA | 1,193,003 | T→C | E257E (GAA→GAG) | mnmA ← | tRNA‑specific 2‑thiouridylase |
| RA | 1,196,220 | C→T | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,232 | C→T | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,245 | T→C | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,247 | A→G | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,241,000 | G→T | L358M (CTG→ATG) | cvrA ← | putative K(+):H(+) antiporter |
| RA | 1,276,204 | T→C | Y472C (TAC→TGC) | narX ← | sensory histidine kinase NarX |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,315,039 | A→G | R62R (CGT→CGC) | yciE ← | DUF892 domain‑containing protein YciE |
| RA | 1,351,196 | (G)7→8 | intergenic (‑157/+211) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase/DUF559 domain‑containing protein YcjD |
| RA | 1,354,805 | A→G | G222G (GGT→GGC) | sapB ← | putrescine ABC exporter membrane subunit SapB |
| RA | 1,361,679 | C→T | A187V (GCG→GTG) | puuD → | gamma‑glutamyl‑gamma‑aminobutyrate hydrolase |
| RA | 1,365,124 | A→G | Y298C (TAC→TGC) | puuB → | gamma‑glutamylputrescine oxidase |
| RA | 1,417,546 | (T)8→7 | coding (218/276 nt) | racC ← | Rac prophage; protein RacC |
| RA | 1,518,258 | A→G | V25A (GTG→GCG) | ydcZ ← | putative inner membrane protein |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,546,404 | A→G | S256P (TCC→CCC) | yddG ← | aromatic amino acid exporter |
| RA | 1,547,482 | C→T | P28S (CCG→TCG) | fdnG → | formate dehydrogenase N subunit alpha |
| RA | 1,554,800 | A→G | G290G (GGT→GGC) | maeA ← | malate dehydrogenase, NAD‑requiring |
| RA | 1,559,542 | T→C | G123G (GGA→GGG) | ddpC ← | putative D,D‑dipeptide ABC transporter membrane subunit DdpC |
| RA | 1,594,132 | (C)8→7 | pseudogene (3955/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,621,165 | T→C | intergenic (‑28/‑167) | eamA ← / → ydeE | cysteine/O‑acetylserine exporter EamA/dipeptide exporter |
| RA | 1,635,023 | T→C | A275A (GCA→GCG) | ydfN ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,635,026 | A→G | H274H (CAT→CAC) | ydfN ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,635,029 | C→T | A273A (GCG→GCA) | ydfN ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,635,032 | G→A | G272G (GGC→GGT) | ydfN ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,635,059 | C→T | S263S (TCG→TCA) | ydfN ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,703,709 | T→C | A200A (GCA→GCG) | ydgJ ← | putative oxidoreductase YdgJ |
| RA | 1,734,017 | T→C | S29G (AGC→GGC) | grxD ← | glutaredoxin 4 |
| RA | 1,757,584 | T→C | V55A (GTT→GCT) | lpp → | murein lipoprotein |
| RA | 1,782,669 | A→G | G425G (GGA→GGG) | ydiS → | putative oxidoreductase with FAD/NAD(P)‑binding domain |
| RA | 1,809,183 | A→G | G17G (GGT→GGC) | yniB ← | uncharacterized protein YniB |
| RA | 1,815,175 | A→G | T437A (ACC→GCC) | katE → | catalase II |
| RA | 1,864,892 | C→T | V249I (GTC→ATC) | yeaE ← | methylglyoxal reductase YeaE |
| RA | 1,871,832 | (G)6→7 | coding (1448/1476 nt) | cdgI → | putative c‑di‑GMP binding protein CdgI |
| 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 | 1,906,058 | T→C | V124A (GTT→GCT) | mntP → | Mn(2(+)) exporter |
| RA | 1,957,452 | T→C | K227K (AAA→AAG) | torY ← | cytochrome c quinol dehydrogenase TorY |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,040,562 | T→C | V27A (GTC→GCC) | msrQ → | periplasmic protein‑L‑methionine sulfoxide reductase heme binding subunit |
| RA | 2,051,390 | T→C | G2151G (GGT→GGC) | yeeJ → | inverse autotransporter adhesin |
| RA | 2,055,218 | T→C | V53A (GTC→GCC) | amn → | AMP nucleosidase |
| RA | 2,071,643 | T→C | G35G (GGT→GGC) | flu → | CP4‑44 prophage; self recognizing antigen 43 (Ag43) autotransporter |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,208,721 | T→C | V252A (GTG→GCG) | yehP → | VWA domain‑containing protein YehP |
| RA | 2,257,717 | A→G | R217R (CGT→CGC) | psuG ← | pseudouridine‑5'‑phosphate glycosidase |
| RA | 2,296,418 | T→C | T203A (ACC→GCC) | ccmB ← | heme trafficking system membrane protein CcmB |
| RA | 2,356,198 | C→G | I226M (ATC→ATG) | glpC → | anaerobic glycerol‑3‑phosphate dehydrogenase subunit C |
| RA | 2,437,329 | T→C | T175A (ACG→GCG) | pdxB ← | erythronate‑4‑phosphate dehydrogenase |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,462,889 | (C)9→8 | intergenic (+243/‑123) | fadL → / → yfdF | long‑chain fatty acid outer membrane channel/bacteriophage T2 receptor/protein YfdF |
| RA | 2,477,402 | T→C | K76K (AAA→AAG) | dsdC ← | DNA‑binding transcriptional dual regulator DsdC |
| RA | 2,496,557 | T→C | Y305H (TAC→CAC) | lpxP → | palmitoleoyl acyltransferase |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,709,986 | G→A | V9V (GTC→GTT) | rpoE ← | RNA polymerase sigma E factor |
| RA | 2,726,130 | T→C | noncoding (59/120 nt) | rrfG ← | 5S ribosomal RNA |
| RA | 2,764,942 | T→C | D71G (GAC→GGC) | abpA ← | CP4‑57 prophage; anti‑bacteriophage protein |
| RA | 2,790,138 | G→A | G53R (GGG→AGG) | lhgO → | L‑2‑hydroxyglutarate oxidase |
| RA | 2,794,400 | G→A | A50T (GCC→ACC) | gabP → | 4‑aminobutyrate:H(+) symporter |
| RA | 2,797,933 | T→C | G138G (GGT→GGC) | ygaP → | thiosulfate sulfurtransferase YgaP |
| 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 | 2,883,629 | T→C | T170T (ACA→ACG) | casA ← | type I‑E CRISPR system Cascade subunit CasA |
| RA | 2,918,146 | A→G | Y414H (TAT→CAT) | gudD ← | D‑glucarate dehydratase |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,959,250 | T→C | D1060G (GAC→GGC) | recC ← | exodeoxyribonuclease V subunit RecC |
| RA | 2,972,860 | (T)7→8 | coding (1003/1194 nt) | lplT ← | lysophospholipid transporter |
| RA | 2,999,680 | (G)7→8 | coding (212/756 nt) | ygeR ← | LysM domain‑containing putative peptidase lipoprotein YgeR |
| RA | 3,008,546 | T→C | V346A (GTT→GCT) | ygeX → | 2,3‑diaminopropionate ammonia‑lyase |
| RA | 3,022,559 | T→C | V415A (GTA→GCA) | xdhD → | fused putative xanthine/hypoxanthine oxidase: molybdopterin‑binding subunit and Fe‑S binding subunit |
| RA | 3,046,673 | T→C | N790S (AAC→AGC) | gcvP ← | glycine decarboxylase |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,141,148 | C→T | E47K (GAG→AAG) | hybD ← | putative hydrogenase 2 maturation protease |
| RA | 3,177,091 | T→C | T64A (ACT→GCT) | yqiB ← | DUF1249 domain‑containing protein YqiB |
| RA | 3,178,919 | A→G | T269A (ACT→GCT) | tolC → | outer membrane channel TolC |
| RA | 3,236,458 | A→G | I167V (ATC→GTC) | ygjP → | putative metal‑dependent hydrolase |
| RA | 3,242,783 | T→C | T178A (ACC→GCC) | uxaA ← | D‑altronate dehydratase |
| RA | 3,349,410 | T→C | S134G (AGC→GGC) | mtgA ← | peptidoglycan glycosyltransferase MtgA |
| RA | 3,350,184 | (C)7→9 | coding (276/654 nt) | elbB ← | low activity glyoxalase ElbB |
| 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 | 3,454,068 | (T)6→7 | coding (1331/1470 nt) | gspA ← | Type II secretion system protein GspA |
| RA | 3,503,667 | A→G | A167A (GCA→GCG) | frlD → | fructoselysine 6‑kinase |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,588,939 | A→G | V81A (GTG→GCG) | ugpC ← | sn‑glycerol 3‑phosphate ABC transporter ATP binding subunit |
| RA | 3,602,893 | T→C | T451A (ACG→GCG) | ftsY ← | signal recognition particle receptor |
| RA | 3,619,269 | A→G | V26V (GTA→GTG) | rhsB → | rhs element protein RhsB |
| RA | 3,619,272 | T→C | R27R (CGT→CGC) | rhsB → | rhs element protein RhsB |
| RA | 3,622,839 | A→G | R1216R (CGA→CGG) | rhsB → | rhs element protein RhsB |
| RA | 3,622,863 | A→G | G1224G (GGA→GGG) | rhsB → | rhs element protein RhsB |
| RA | 3,632,011 | T→C | T194A (ACA→GCA) | yhiJ ← | DUF4049 domain‑containing protein YhiJ |
| RA | 3,695,943 | T→C | pseudogene (43/753 nt) | bcsQ ← | cellulose biosynthesis protein |
| RA | 3,717,584 | T→C | L92P (CTG→CCG) | ghrB → | glyoxylate reductase |
| RA | 3,737,150 | Δ1 bp | coding (28/825 nt) | bax ← | putative glycoside hydrolase Bax |
| RA | 3,748,607 | G→A | D11N (GAC→AAC) | sgbH → | 3‑keto‑L‑gulonate‑6‑phosphate decarboxylase SgbH |
| RA | 3,763,974 | 2 bp→GC | coding (1792‑1793/4134 nt) | rhsA → | rhs element protein RhsA |
| RA | 3,763,992 | G→A | A604T (GCC→ACC) | rhsA → | rhs element protein RhsA |
| RA | 3,779,571 | T→C | V173A (GTC→GCC) | lldR → | DNA‑binding transcriptional dual regulator LldR |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,841,006 | T→C | N245S (AAC→AGC) | nepI ← | purine ribonucleoside exporter |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,905,639 | (A)9→10 | intergenic (‑42/+92) | bglF ← / ← bglG | beta‑glucoside specific PTS enzyme II/BglG kinase/BglG phosphatase/transcriptional antiterminator BglG |
| RA | 3,925,446 | A→G | V63A (GTG→GCG) | mnmG ← | 5‑carboxymethylaminomethyluridine‑tRNA synthase subunit MnmG |
| RA | 3,928,843 | C→T | G254D (GGT→GAT) | viaA ← | protein ViaA |
| RA | 3,931,183 | (G)7→9 | intergenic (‑90/‑133) | ravA ← / → kup | regulatory ATPase RavA/K(+):H(+) symporter Kup |
| RA | 3,980,957 | (G)6→7 | coding (71/1386 nt) | yifK → | putative transporter YifK |
| RA | 4,034,211 | T→C | V356A (GTG→GCG) | trkH → | K(+) transporter TrkH |
| RA | 4,092,336 | T→C | T11A (ACC→GCC) | frvB ← | putative PTS enzyme IIBC component FrvB |
| MC | 4,094,443 | Δ184 bp | between other | rhaD ← / ← rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| RA | 4,095,004 | A→G | F327L (TTC→CTC) | rhaA ← | L‑rhamnose isomerase |
| RA | 4,173,359 | A→G | Y93C (TAC→TGC) | birA → | DNA‑binding transcriptional repressor/biotin‑[acetyl‑CoA‑carboxylase] ligase BirA |
| RA | 4,182,388 | G→A | E382K (GAA→AAA) | rpoB → | RNA polymerase subunit beta |
| RA | 4,264,347 | G→A | A12T (GCT→ACT) | dnaB → | replicative DNA helicase |
| RA | 4,293,106 | (G)7→8 | coding (1595/1659 nt) | nrfE → | putative cytochrome c‑type biogenesis protein NrfE |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,329,894 | (G)6→5 | coding (535/879 nt) | yjcZ → | uncharacterized protein YjcZ |
| RA | 4,364,253 | T→C | T264A (ACC→GCC) | dsbD ← | protein disulfide oxidoreductase ‑ DsbDreduced |
| RA | 4,410,053 | (T)9→8 | intergenic (+47/‑80) | rlmB → / → yjfI | 23S rRNA 2'‑O‑ribose G2251 methyltransferase/conserved protein YjfI |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,473,717 | C→T | A113T (GCC→ACC) | bdcA ← | c‑di‑GMP‑binding biofilm dispersal mediator protein |
| RA | 4,493,576 | C→T | M277I (ATG→ATA) | idnD ← | L‑idonate 5‑dehydrogenase |
| RA | 4,565,526 | C→T | D109N (GAC→AAC) | yjiM ← | putative dehydratase subunit |
| JC | 4,606,094 | (G)8→11 | noncoding (72/87 nt) | leuV ← | tRNA‑Leu |
| RA | 4,633,830 | A→G | T12A (ACG→GCG) | ytjC → | putative phosphatase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196275 | 1211422 | 15148 | 16 [14] | [14] 15 | [icd]–[icdC] | [icd],ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,oweE,ymfN,aaaE,ymfR,beeE,jayE,ymfQ,ycfK,tfaP,tfaE,stfE,pinE,mcrA,[icdC] |
| * | * | ÷ | NC_000913 | 1633059–1633220 | 1634976–1634642 | 1423–1918 | 16 [14] | [13] 16 | ydfK–[ydfN] | ydfK,pinQ,tfaQ,[ydfN] |
| * | * | ÷ | NC_000913 | 3423770–3424234 | 3424530–3424240 | 7–761 | 16 [14] | [14] 18 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3621202–3622297 | 3622783–3622379 | 83–1582 | 16 [13] | [13] 16 | rhsB | rhs element protein RhsB |
| * | * | ÷ | NC_000913 | 4035853–4037092 | 4040600–4039392 | 2301–4748 | 15 [14] | [14] 15 | [rrsA]–[rrfA] | [rrsA],ileT,alaT,rrlA,[rrfA] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 3363001 = | 101 (1.680) | 97 (1.620) | 49/274 | 0.1 | 65.7% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 1 (0.020) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 58 (0.960) | 38/276 | 0.4 | 96.7% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 2 (0.030) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||