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 | 22,891 | C→T | R167R (CGC→CGT) | ileS → | isoleucine‑‑tRNA ligase |
| RA | 61,392 | A→G | Y625H (TAT→CAT) | rapA ← | RNA polymerase‑binding ATPase and RNAP recycling factor |
| RA | 91,264 | A→G | D78G (GAC→GGC) | ftsL → | cell division protein FtsL |
| RA | 92,082 | A→G | T224A (ACT→GCT) | ftsI → | peptidoglycan DD‑transpeptidase FtsI |
| RA | 97,308 | T→C | G74G (GGT→GGC) | murD → | UDP‑N‑acetylmuramoyl‑L‑alanine‑‑D‑glutamate ligase |
| RA | 213,575 | T→C | G415G (GGT→GGC) | tilS → | tRNA(Ile)‑lysidine synthetase |
| RA | 217,026 | (A)7→8 | intergenic (‑23/+31) | yaeF ← / ← proS | peptidase C92 family protein/proline‑‑tRNA ligase |
| RA | 236,911 | T→C | intergenic (+113/‑20) | dnaQ → / → aspV | DNA polymerase III subunit epsilon/tRNA‑Asp |
| RA | 247,673 | A→G | T13A (ACA→GCA) | rayT → | REP‑associated tyrosine transposase |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 268,138 | C→T | V275M (GTG→ATG) | ykfA ← | CP4‑6 prophage; putative GTP‑binding protein YkfA |
| RA | 271,248 | A→G | T216A (ACA→GCA) | insI‑1 → | IS30 transposase |
| RA | 326,192 | A→G | R352R (CGT→CGC) | betA ← | choline dehydrogenase |
| RA | 372,774 | A→G | E220E (GAA→GAG) | mhpD → | 2‑hydroxypentadienoate hydratase |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 388,666 | C→T | intergenic (+20/+87) | tauD → / ← hemB | taurine dioxygenase/porphobilinogen synthase |
| RA | 469,238 | A→G | D123G (GAC→GGC) | mdlA → | ABC transporter family protein MdlA |
| RA | 518,198 | A→G | F28L (TTC→CTC) | cnoX ← | chaperedoxin |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 618,845 | T→C | L198L (TTG→CTG) | fepE → | polysaccharide co‑polymerase family protein FepE |
| RA | 642,281 | A→G | E65G (GAA→GGA) | ybdR → | putative Zn(2(+))‑dependent alcohol dehydrogenase YbdR |
| RA | 677,528 | T→C | G38G (GGT→GGC) | djlB → | putative chaperone |
| RA | 677,922 | A→G | T170A (ACC→GCC) | djlB → | putative chaperone |
| RA | 707,786 | G→A | intergenic (+29/‑548) | glnS → / → chiP | glutamine‑‑tRNA ligase/chitobiose outer membrane channel |
| RA | 736,709 | +C | intergenic (+10/‑191) | ybfQ → / → ybfL | inactive transposase YbfQ/putative transposase YbfL |
| RA | 796,417 | T→C | Y186H (TAT→CAT) | modB → | molybdate ABC transporter membrane subunit |
| RA | 877,281 | G→A | A252V (GCA→GTA) | rimO ← | ribosomal protein S12 methylthiotransferase RimO |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 920,764 | T→C | Y140H (TAT→CAT) | macB → | ABC‑type tripartite efflux pump ATP binding/membrane subunit |
| RA | 921,992 | C→T | T549I (ACC→ATC) | macB → | ABC‑type tripartite efflux pump ATP binding/membrane subunit |
| RA | 927,208 | G→A | S75S (AGC→AGT) | aat ← | leucyl/phenylalanyl‑tRNA‑‑protein transferase |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 975,711 | A→G | L30L (TTA→TTG) | mukE → | chromosome partitioning protein MukE |
| RA | 986,448 | A→G | Y179H (TAC→CAC) | ompF ← | outer membrane porin F |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,040,030 | A→G | K245K (AAA→AAG) | appB → | cytochrome bd‑II ubiquinol oxidase subunit II |
| RA | 1,059,533 | A→G | H93R (CAC→CGC) | torA → | trimethylamine N‑oxide reductase 1 |
| RA | 1,089,445 | (G)5→4 | coding (413/2019 nt) | pgaB ← | poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine N‑deacetylase and beta‑1,6 glycoside hydrolase |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,151,093 | A→G | T142A (ACC→GCC) | fabG → | 3‑oxoacyl‑[acyl‑carrier‑protein] reductase FabG |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,244,726 | A→G | intergenic (‑199/‑2) | ycgR ← / → ymgE | flagellar brake protein YcgR/PF04226 family protein YmgE |
| RA | 1,259,759 | A→G | S349P (TCC→CCC) | dauA ← | aerobic C4‑dicarboxylate transporter DauA |
| RA | 1,270,719 | (C)5→6 | intergenic (+259/+30) | rdlC → / ← chaA | small regulatory antisense RNA RdlC/Na(+)/K(+):H(+) antiporter ChaA |
| RA | 1,287,842 | T→C | A261A (GCA→GCG) | purU ← | formyltetrahydrofolate deformylase |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,405,392 | A→G | T218A (ACG→GCG) | abgR → | putative LysR‑type DNA‑binding transcriptional regulator AbgR |
| RA | 1,435,363 | A→G | V86A (GTG→GCG) | uspF ← | nucleotide binding filament protein |
| RA | 1,436,241 | T→C | Y218C (TAC→TGC) | ompN ← | outer membrane porin N |
| RA | 1,486,541 | A→G | T1161A (ACG→GCG) | hrpA → | ATP‑dependent RNA helicase HrpA |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,620,380 | A→G | V253A (GTA→GCA) | eamA ← | cysteine/O‑acetylserine exporter EamA |
| RA | 1,621,699 | A→G | D123G (GAC→GGC) | ydeE → | dipeptide exporter |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,647,076 | T→C | intergenic (+339/+98) | flxA → / ← ydfW | Qin prophage; protein FlxA/Qin prophage; uncharacterized protein YdfW |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,742,612 | T→C | T211A (ACA→GCA) | ribC ← | riboflavin synthase |
| RA | 1,793,133 | C→T | L142L (TTG→TTA) | btuD ← | vitamin B12 ABC transporter ATP binding subunit |
| RA | 1,817,811 | Δ1 bp | coding (690/1353 nt) | chbF ← | monoacetylchitobiose‑6‑phosphate hydrolase |
| 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 | 1,906,870 | G→A | A64V (GCC→GTC) | rlmA ← | 23S rRNA m(1)G745 methyltransferase |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,040,269 | A→G | P264P (CCA→CCG) | msrP → | periplasmic protein‑L‑methionine sulfoxide reductase catalytic subunit |
| RA | 2,057,676 | (C)7→8 | intergenic (+102/+351) | yeeN → / ← asnW | putative transcriptional regulator YeeN/tRNA‑Asn |
| RA | 2,074,362 | (C)6→7 | coding (2824/3120 nt) | flu → | CP4‑44 prophage; self recognizing antigen 43 (Ag43) autotransporter |
| RA | 2,107,058 | A→G | L57L (TTG→CTG) | wbbH ← | putative O‑antigen polymerase |
| RA | 2,162,335 | G→A | G291D (GGC→GAC) | mdtD → | putative multidrug efflux pump MdtD |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| JC JC | 2,237,642 | IS5 (–) +4 bp | coding (109‑112/1011 nt) | mglC ← | D‑galactose/methyl‑galactoside ABC transporter membrane subunit |
| RA | 2,246,532 | T→C | T80A (ACG→GCG) | cirA ← | ferric dihyroxybenzoylserine outer membrane transporter |
| RA | 2,262,214 | T→C | D51G (GAC→GGC) | fruK ← | 1‑phosphofructokinase |
| RA | 2,297,107 | T→C | I180V (ATT→GTT) | ccmA ← | heme trafficking system ATP‑binding protein |
| RA | 2,363,421 | T→C | G71G (GGA→GGG) | yfaY ← | IPR008135 CinA family protein YfaY |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,475,069 | T→C | V29A (GTT→GCT) | yfdR → | CPS‑53 (KpLE1) prophage; 5'‑deoxynucleotidase |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,542,969 | A→G | F187S (TTC→TCC) | cysP ← | thiosulfate/sulfate ABC transporter periplasmic binding protein CysP |
| RA | 2,674,352 | G→A | H113Y (CAC→TAC) | yphB ← | putative aldose 1‑epimerase YphB |
| RA | 2,680,114 | G→A | P878S (CCG→TCG) | yphG ← | DUF5107 domain‑containing protein YphG |
| RA | 2,720,390 | A→G | K146K (AAA→AAG) | patZ → | peptidyl‑lysine acetyltransferase |
| RA | 2,745,777 | A→G | F48L (TTT→CTT) | rimM ← | ribosome maturation factor RimM |
| RA | 2,755,737 | C→T | noncoding (145/363 nt) | ssrA → | tmRNA |
| RA | 2,763,764 | A→G | F464L (TTT→CTT) | abpA ← | CP4‑57 prophage; anti‑bacteriophage protein |
| RA | 2,789,783 | G→A | E267K (GAA→AAA) | csiD → | PF08943 family protein CsiD |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,811,367 | T→C | intergenic (+67/‑60) | mprA → / → emrA | DNA‑binding transcriptional repressor MprA/multidrug efflux pump membrane fusion protein EmrA |
| RA | 2,838,784 | A→G | C161R (TGC→CGC) | ascG ← | DNA‑binding transcriptional repressor AscG |
| RA | 2,844,492 | C→T | T87T (ACG→ACA) | hycF ← | formate hydrogenlyase subunit HycF |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,899,590 | A→G | D228D (GAT→GAC) | ygcW ← | putative deoxygluconate dehydrogenase |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,975,132 | T→C | T295A (ACC→GCC) | aas ← | acyltransferase |
| RA | 2,977,601 | G→A | E335K (GAG→AAG) | galR → | DNA‑binding transcriptional dual regulator GalR |
| RA | 2,996,027 | T→C | pseudogene (334/399 nt) | ygeO ← | putative uncharacterized protein YgeO |
| RA | 3,001,304 | (G)7→8 | coding (960/2259 nt) | xdhA → | putative xanthine dehydrogenase molybdenum‑binding subunit XdhA |
| RA | 3,007,752 | T→C | G81G (GGT→GGC) | ygeX → | 2,3‑diaminopropionate ammonia‑lyase |
| RA | 3,019,754 | T→C | G198G (GGT→GGC) | ssnA → | putative aminohydrolase |
| RA | 3,022,809 | T→C | D498D (GAT→GAC) | xdhD → | fused putative xanthine/hypoxanthine oxidase: molybdopterin‑binding subunit and Fe‑S binding subunit |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,070,755 | G→A | R164C (CGC→TGC) | fbaA ← | fructose‑bisphosphate aldolase class II |
| RA | 3,080,055 | T→C | E527E (GAA→GAG) | tktA ← | transketolase 1 |
| RA | 3,172,137 | (A)7→6 | coding (75/333 nt) | ygiZ ← | conserved inner membrane protein YgiZ |
| RA | 3,174,743 | A→G | G218G (GGT→GGC) | parE ← | DNA topoisomerase IV subunit B |
| RA | 3,293,009 | G→A | C109C (TGC→TGT) | rsmI ← | 16S rRNA 2'‑O‑ribose C1402 methyltransferase |
| RA | 3,320,052 | A→G | V521A (GTG→GCG) | yhbX ← | putative hydrolase, inner membrane |
| 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 | 3,424,742 | T→C | noncoding (2042/2904 nt) | rrlD ← | 23S ribosomal RNA |
| RA | 3,483,979 | A→G | S260G (AGC→GGC) | yheT → | putative hydrolase YheT |
| RA | 3,497,915 | T→C | L30L (TTG→CTG) | cysG → | siroheme synthase |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,591,066 | G→A | T420T (ACC→ACT) | ugpB ← | sn‑glycerol 3‑phosphate ABC transporter periplasmic binding protein |
| RA | 3,624,042 | (G)6→7 | intergenic (+260/‑336) | yhhH → / → yhhI | PF15631 family protein YhhH/putative transposase |
| RA | 3,786,972 | T→C | A45A (GCT→GCC) | envC → | murein hydrolase activator EnvC |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,823,068 | T→C | R223R (CGT→CGC) | spoT → | bifunctional (p)ppGpp synthase/hydrolase SpoT |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,867,173 | T→C | T84A (ACC→GCC) | ibpA ← | small heat shock protein IbpA |
| RA | 4,089,844 | T→C | E4E (GAA→GAG) | frvR ← | putative transcriptional regulator FrvR |
| RA | 4,148,814 | A→G | R484R (CGT→CGC) | eptC ← | phosphoethanolamine transferase EptC |
| RA | 4,200,626 | A→G | M21V (ATG→GTG) | yjaH → | DUF1481 domain‑containing protein YjaH |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,326,444 | A→G | G97G (GGT→GGC) | yjdM ← | conserved protein YjdM |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,469,825 | A→G | N734S (AAC→AGC) | mgtA → | Mg(2(+)) importing P‑type ATPase |
| RA | 4,472,714 | T→C | intergenic (‑181/+100) | pyrL ← / ← yjgH | pyrBI operon leader peptide/RutC family protein YjgH |
| RA | 4,513,286 | C→T | A42T (GCC→ACC) | fecC ← | ferric citrate ABC transporter membrane subunit FecC |
| RA | 4,516,827 | C→T | A297A (GCG→GCA) | fecR ← | regulator for fec operon, periplasmic |
| RA | 4,520,052 | T→C | E91E (GAA→GAG) | yjhU ← | KpLE2 phage‑like element; putative DNA‑binding transcriptional regulator YjhU |
| RA | 4,521,565 | (A)6→7 | coding (456/1350 nt) | yjhF ← | KpLE2 phage‑like element; putative transporter YjhF |
| RA | 4,561,280 | (A)7→6 | coding (351/555 nt) | kptA → | RNA 2'‑phosphotransferase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423762–3424234 | 3424523–3424238 | 5–762 | 16 [15] | [11] 16 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3751932 | 3751983 | 52 | 16 [13] | [14] 16 | yiaT/yiaU | outer membrane protein YiaT/putative LysR‑type DNA‑binding transcriptional regulator YiaU |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 54 (0.880) | 26 (0.480) | 23/246 | 1.1 | 33.8% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 54 (0.990) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 54 (0.880) | 13 (0.240) | 12/246 | 2.7 | 20.3% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 54 (0.990) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 3363001 = | 114 (1.850) | 81 (1.330) | 48/276 | 0.1 | 58.2% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 3 (0.050) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 74 (1.200) | 49/278 | 0.1 | 93.7% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 5 (0.080) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 4542690 | 36 (0.590) | 25 (0.430) | 19/260 | 1.7 | 41.8% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 36 (0.630) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||