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 | 42,594 | T→C | G64G (GGT→GGC) | fixA → | putative electron transfer flavoprotein FixA |
| RA | 71,603 | T→C | L85L (TTG→CTG) | yabI → | DedA family protein YabI |
| RA | 109,503 | A→G | T409A (ACC→GCC) | secA → | protein translocation ATPase |
| RA | 135,426 | A→G | S53P (TCA→CCA) | speD ← | S‑adenosylmethionine decarboxylase proenzyme |
| RA | 151,130 | A→G | V157A (GTA→GCA) | yadK ← | putative fimbrial protein YadK |
| RA | 183,533 | T→C | R357R (CGT→CGC) | cdaR → | DNA‑binding transcriptional activator CdaR |
| RA | 215,452 | T→C | F62L (TTC→CTC) | nlpE → | lipoprotein NlpE |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 267,546 | A→G | Y154H (TAT→CAT) | yafZ ← | CP4‑6 prophage; conserved protein YafZ |
| RA | 308,820 | A→G | S171S (AGT→AGC) | ecpC ← | putative fimbrial usher protein EcpC |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 508,648 | C→G | intergenic (+89/+227) | ybaQ → / ← copA | putative DNA‑binding transcriptional regulator YbaQ/Cu(+) exporting P‑type ATPase |
| RA | 508,670 | T→C | intergenic (+111/+205) | ybaQ → / ← copA | putative DNA‑binding transcriptional regulator YbaQ/Cu(+) exporting P‑type ATPase |
| RA | 509,462 | +T | coding (1918/2505 nt) | copA ← | Cu(+) exporting P‑type ATPase |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 546,079 | T→C | E95E (GAA→GAG) | allD ← | ureidoglycolate dehydrogenase |
| RA | 593,357 | T→C | T472A (ACA→GCA) | cusS ← | sensory histidine kinase CusS |
| RA | 601,989 | A→G | T11A (ACT→GCT) | pheP → | phenylalanine:H(+) symporter PheP |
| RA | 723,528 | (T)8→7 | coding (887/2685 nt) | kdpD ← | sensory histidine kinase KdpD |
| RA | 766,957 | (G)6→7 | coding (974/1977 nt) | mngA → | 2‑O‑alpha‑mannosyl‑D‑glycerate specific PTS enzyme II |
| RA | 797,143 | A→G | D197G (GAC→GGC) | modC → | molybdate ABC transporter ATP binding subunit |
| RA | 845,630 | (T)6→5 | intergenic (‑150/+111) | ybiO ← / ← glnQ | moderate conductance mechanosensitive channel/L‑glutamine ABC transporter 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 | 993,892 | A→G | S51S (AGT→AGC) | ssuB ← | aliphatic sulfonate ABC transporter ATP binding subunit |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,029,019 | A→G | G317G (GGT→GGC) | rlmI ← | 23S rRNA m(5)C1962 methyltransferase |
| RA | 1,043,639 | T→C | D191G (GAC→GGC) | etk ← | protein‑tyrosine kinase Etk |
| RA | 1,071,284 | A→G | L161P (CTG→CCG) | rutD ← | putative aminoacrylate hydrolase |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,146,094 | C→T | D168N (GAT→AAT) | yceF ← | m(7)GTP pyrophosphatase |
| RA | 1,160,689 | T→C | N288S (AAC→AGC) | fhuE ← | ferric coprogen/ferric rhodotorulic acid outer membrane transporter |
| RA | 1,182,791 | A→G | A13A (GCT→GCC) | potD ← | spermidine preferential ABC transporter periplasmic binding protein |
| RA | 1,217,023 | A→G | intergenic (+27/‑305) | ymgC → / → pdeG | protein YmgC/putative c‑di‑GMP phosphodiesterase PdeG |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,232,886 | A→G | C49R (TGC→CGC) | dsbB ← | protein thiol:quinone oxidoreductase DsbB |
| RA | 1,261,786 | G→A | A30A (GCC→GCT) | prs ← | ribose‑phosphate diphosphokinase |
| RA | 1,281,216 | G→A | V451V (GTG→GTA) | narG → | nitrate reductase A subunit alpha |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,351,421 | A→G | S114P (TCA→CCA) | ycjD ← | DUF559 domain‑containing protein YcjD |
| RA | 1,420,167 | T→C | K25K (AAA→AAG) | racR ← | Rac prophage; DNA‑binding transcriptional repressor RacR |
| RA | 1,424,378 | T→C | C199C (TGT→TGC) | trkG → | Rac prophage; K(+) transporter TrkG |
| RA | 1,502,450 | A→G | intergenic (+295/‑7) | tehB → / → ydcL | tellurite methyltransferase/DUF3313 domain‑containing lipoprotein YdcL |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,543,164 | A→G | G299G (GGT→GGC) | narU ← | nitrate/nitrite transporter NarU |
| RA | 1,627,366 | A→G | N5N (AAT→AAC) | dcp ← | peptidyl‑dipeptidase Dcp |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,714,326 | (T)9→8 | intergenic (+55/‑51) | dtpA → / → gstA | dipeptide/tripeptide:H(+) symporter DtpA/glutathione S‑transferase GstA |
| JC | 1,769,478 | (G)7→10 | coding (405/1113 nt) | ydiK → | putative transporter YdiK |
| RA | 1,852,712 | C→T | G423D (GGT→GAT) | 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 | 1,933,321 | G→A | G428G (GGC→GGT) | edd ← | phosphogluconate dehydratase |
| RA | 1,966,676 | A→G | V121A (GTA→GCA) | cheZ ← | chemotaxis protein CheZ |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 1,996,183 | T→C | N217S (AAC→AGC) | sdiA ← | DNA‑binding transcriptional dual regulator SdiA |
| RA | 2,028,264 | T→C | Y36C (TAC→TGC) | yodC ← | protein YodC |
| RA | 2,053,682 | A→G | T14A (ACG→GCG) | shiA → | shikimate:H(+) symporter |
| RA | 2,123,646 | T→C | H292R (CAC→CGC) | cpsB ← | mannose‑1‑phosphate guanylyltransferase |
| RA | 2,157,427 | T→C | V722A (GTT→GCT) | mdtB → | multidrug efflux pump RND permease subunit MdtB |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,174,447 | C→T | R40R (CGG→CGA) | gatB ← | galactitol‑specific PTS enzyme IIB component |
| RA | 2,237,776 | T→C | H505R (CAC→CGC) | mglA ← | D‑galactose/methyl‑galactoside ABC transporter ATP binding subunit |
| RA | 2,305,395 | C→T | G454R (GGG→AGG) | mqo ← | malate:quinone oxidoreductase |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,517,553 | T→C | T94A (ACG→GCG) | pdeA ← | putative c‑di‑GMP phosphodiesterase PdeA |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,527,966 | A→G | V65A (GTC→GCC) | ypeB ← | PF12843 family protein YpeB |
| RA | 2,554,556 | (C)5→4 | coding (627/1053 nt) | eutR ← | putative AraC‑type transcriptional regulator EutR |
| RA | 2,607,885 | Δ1 bp | coding (969/1581 nt) | hyfF → | hydrogenase 4 component F |
| RA | 2,616,960 | T→C | R289R (CGT→CGC) | bepA → | beta‑barrel assembly‑enhancing protease |
| RA | 2,634,737 | T→C | V169A (GTG→GCG) | xseA → | exodeoxyribonuclease VII subunit XseA |
| RA | 2,666,070 | A→G | A212A (GCA→GCG) | csiE → | stationary phase inducible protein CsiE |
| RA | 2,710,284 | C→T | intergenic (‑120/‑136) | rseD ← / → nadB | rpoE leader peptide/L‑aspartate oxidase |
| RA | 2,734,543 | (C)8→9 | coding (492/732 nt) | pgeF ← | polyphenol oxidase YfiH |
| RA | 2,756,508 | T→C | V117A (GTG→GCG) | intA → | CP4‑57 prophage; integrase |
| RA | 2,805,081 | T→C | G89G (GGT→GGC) | proV → | glycine betaine ABC transporter ATP binding subunit ProV |
| RA | 2,807,957 | T→C | F276L (TTT→CTT) | proX → | glycine betaine ABC transporter periplasmic binding protein ProX |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,834,249 | T→C | V113A (GTC→GCC) | norW → | NADH:flavorubredoxin reductase |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,860,816 | T→C | H140R (CAC→CGC) | ygbI ← | putative DeoR‑type DNA‑binding transcriptional regulator YgbI |
| RA | 2,924,165 | (A)7→8 | noncoding (360/369 nt) | csrB ← | small regulatory RNA CsrB |
| RA | 2,924,974 | T→C | T103A (ACC→GCC) | syd ← | SecY‑interacting protein |
| RA | 2,928,467 | A→G | N80S (AAC→AGC) | sdaC → | serine:H(+) symporter SdaC |
| RA | 2,941,825 | A→T | I248N (ATC→AAC) | gcvA ← | DNA‑binding transcriptional dual regulator GcvA |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,999,680 | (G)7→6 | coding (212/756 nt) | ygeR ← | LysM domain‑containing putative peptidase lipoprotein YgeR |
| RA | 3,019,938 | A→G | T260A (ACG→GCG) | ssnA → | putative aminohydrolase |
| RA | 3,059,769 | A→G | Y6C (TAC→TGC) | argP → | DNA‑binding transcriptional dual regulator ArgP |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,147,044 | T→C | pseudogene (648/836 nt) | yghX ← | putative hydrolase fragment |
| RA | 3,230,363 | T→C | S492S (TCT→TCC) | ygjK → | glycoside hydrolase |
| RA | 3,343,349 | G→A | A172T (GCC→ACC) | lptC → | lipopolysaccharide transport system protein LptC |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,379,266 | (C)7→9 | coding (732/1128 nt) | zapE ← | cell division factor ZapE with ATPase activity |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,403,864 | C→T | A127A (GCC→GCT) | yhdH → | acrylyl‑CoA reductase |
| RA | 3,405,503 | T→C | I23T (ATT→ACT) | accB → | biotin carboxyl carrier protein |
| RA | 3,469,228 | A→G | V209A (GTT→GCT) | chiA ← | endochitinase |
| RA | 3,523,234 | A→G | T122A (ACC→GCC) | mrcA → | peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcA |
| RA | 3,544,647 | T→C | E66E (GAA→GAG) | bioH ← | pimeloyl‑acyl carrier protein methyl ester esterase |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,598,987 | A→G | G224G (GGT→GGC) | livJ ← | branched chain amino acid/phenylalanine ABC transporter periplasmic binding protein |
| RA | 3,599,363 | T→C | H99R (CAC→CGC) | livJ ← | branched chain amino acid/phenylalanine ABC transporter periplasmic binding protein |
| RA | 3,617,376 | C→A | A121D (GCC→GAC) | nikD → | Ni(2(+)) ABC transporter ATP binding subunit NikD |
| RA | 3,663,950 | T→C | R223R (CGA→CGG) | gadW ← | DNA‑binding transcriptional dual regulator GadW |
| RA | 3,810,273 | T→C | V150A (GTC→GCC) | coaD → | pantetheine‑phosphate adenylyltransferase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,838,253 | T→C | G2G (GGT→GGC) | yicL → | putative inner membrane protein |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,889,005 | T→C | G92G (GGT→GGC) | tnaA → | tryptophanase |
| RA | 3,905,561 | (C)5→6 | coding (37/1878 nt) | bglF ← | beta‑glucoside specific PTS enzyme II/BglG kinase/BglG phosphatase |
| RA | 3,982,684 | (C)8→9 | noncoding (79/87 nt) | leuT → | tRNA‑Leu |
| RA | 4,110,285 | T→C | V119A (GTT→GCT) | cdh → | CDP‑diacylglycerol diphosphatase |
| RA | 4,122,079 | C→T | G70D (GGC→GAC) | hslV ← | peptidase component of the HslVU protease |
| RA | 4,188,760 | T→C | G1137G (GGT→GGC) | rpoC → | RNA polymerase subunit beta' |
| RA | 4,207,132 | A→G | V134A (GTG→GCG) | purH ← | bifunctional AICAR transformylase/IMP cyclohydrolase |
| RA | 4,259,896 | A→G | S36S (AGT→AGC) | zur ← | DNA‑binding transcriptional repressor Zur |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,309,297 | A→G | V58A (GTT→GCT) | alsC ← | D‑allose ABC transporter membrane subunit |
| RA | 4,341,051 | A→G | V193A (GTT→GCT) | melR ← | DNA‑binding transcriptional dual regulator MelR |
| RA | 4,385,556 | T→C | L55P (CTC→CCC) | yjeN → | protein YjeN |
| RA | 4,386,896 | A→G | S825S (AGT→AGC) | mscM ← | miniconductance mechanosensitive channel MscM |
| RA | 4,397,867 | C→T | Y152Y (TAC→TAT) | mutL → | DNA mismatch repair protein MutL |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,499,424 | G→A | G277D (GGT→GAT) | insD‑6 → | KpLE2 phage‑like element; IS2 insertion element protein InsB |
| RA | 4,528,262 | C→T | G219D (GGC→GAC) | sgcQ ← | KpLE2 phage‑like element; putative nucleoside triphosphatase |
| RA | 4,533,630 | A→G | L52P (CTA→CCA) | yjhQ ← | KpLE2 phage‑like element; putative acetyltransferase TopAI antitoxin YjhQ |
| RA | 4,586,834 | A→G | intergenic (‑73/‑115) | hsdR ← / → mrr | type I restriction enzyme EcoKI endonuclease component/methylated adenine and cytosine restriction protein |
| RA | 4,588,280 | A→G | F196L (TTC→CTC) | yjiA ← | P‑loop guanosine triphosphatase |
| RA | 4,589,494 | A→G | Y596H (TAC→CAC) | btsT ← | pyruvate:H(+) symporter |
| RA | 4,589,505 | T→C | K592R (AAG→AGG) | btsT ← | pyruvate:H(+) symporter |
| RA | 4,606,215 | (G)8→9 | noncoding (72/87 nt) | leuP ← | tRNA‑Leu |
| RA | 4,620,155 | T→C | F185L (TTC→CTC) | deoB → | phosphopentomutase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1433751–1434067 | 1434241–1434075 | 9–491 | 18 [16] | [16] 17 | ynaE | ynaE |
| * | * | ÷ | NC_000913 | 3423776–3424525 | 3424525 | 1–750 | 17 [16] | [8] 18 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 1 (0.010) | 71 (1.170) | 47/244 | 0.2 | 96.7% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 4 (0.070) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 1 (0.010) | 48 (0.790) | 35/244 | 0.5 | 95.2% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 4 (0.070) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 3363001 = | 101 (1.470) | 100 (1.470) | 59/274 | 0.1 | 66.0% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 3 (0.040) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 72 (1.050) | 48/276 | 0.3 | 96.0% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 3 (0.040) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||