mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| JC JC | 57,276 | IS2 (+) +5 bp | intergenic (‑167/‑84) | lptD ← / → djlA | lipopolysaccharide assembly protein LptD/co‑chaperone protein DjlA |
| RA | 71,134 | G→A | G250S (GGT→AGT) | araC → | DNA‑binding transcriptional dual regulator AraC |
| RA | 74,872 | C→T | L203L (CTG→CTA) | thiB ← | thiamine ABC transporter periplasmic binding protein |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 315,391 | C→T | A34V (GCC→GTC) | insE1 → | IS3 element protein InsE |
| RA | 324,526 | C→T | intergenic (+73/+170) | ykgG → / ← ykgH | DUF162 domain‑containing lactate utilization protein YkgG/uncharacterized protein YkgH |
| RA | 334,755 | C→T | A90T (GCG→ACG) | yahC ← | uncharacterized protein YahC |
| RA | 351,119 | C→T | P370S (CCT→TCT) | prpC → | 2‑methylcitrate synthase |
| RA | 358,335 | C→T | S119N (AGC→AAC) | cynR ← | DNA‑binding transcriptional dual regulator CynR |
| RA | 370,161 | C→T | R517R (CGC→CGT) | mhpA → | 3‑(3‑hydroxyphenyl)propanoate hydroxylase |
| RA | 398,532 | C→T | P221S (CCC→TCC) | yaiW → | surface‑exposed outer membrane lipoprotein |
| RA | 407,365 | C→T | intergenic (+195/‑63) | yaiA → / → aroM | protein YaiA/protein AroM |
| RA | 438,694 | C→T | G495D (GGC→GAC) | dxs ← | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase |
| RA | 446,923 | C→T | A261A (GCG→GCA) | cyoE ← | heme O synthase |
| RA | 448,935 | C→T | E569E (GAG→GAA) | cyoB ← | cytochrome bo3 subunit 1 |
| RA | 463,208 | C→T | P432S (CCG→TCG) | ppiD → | periplasmic folding chaperone |
| RA | 480,023 | C→T | intergenic (‑105/+67) | maa ← / ← hha | maltose O‑acetyltransferase/hemolysin expression‑modulating protein Hha |
| RA | 497,134 | C→T | intergenic (+140/‑41) | htpG → / → adk | chaperone protein HtpG/adenylate kinase |
| RA | 547,889 | C→T | L404F (CTC→TTC) | fdrA → | putative oxamate carbamoyltransferase FdrA |
| RA | 557,635 | A→T | L36Q (CTG→CAG) | folD ← | bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase |
| JC JC | 568,449 | IS2 (–) +5 bp | coding (135‑139/333 nt) | emrE → | multidrug/betaine/choline efflux transporter EmrE |
| RA | 577,424 | G→A | T9T (ACG→ACA) | essD → | putative phage lysis protein |
| RA | 585,900 | C→T | intergenic (‑267/+247) | ompT ← / ← envY | omptin family outer membrane protease OmpT/DNA‑binding transcriptional activator EnvY |
| RA | 587,830 | C→T | G51D (GGC→GAC) | ybcH ← | putative exopolysaccharide secretion system auxiliary component |
| RA | 587,879 | C→T | V35I (GTT→ATT) | ybcH ← | putative exopolysaccharide secretion system auxiliary component |
| RA | 590,620 | G→A | P112L (CCA→CTA) | nfrA ← | exopolysaccharide secretion system outer membrane protein NfrA |
| RA | 601,732 | G→A | E1007K (GAG→AAG) | cusA → | copper/silver export system RND permease |
| RA | 603,023 | G→A | V355V (GTG→GTA) | pheP → | phenylalanine:H(+) symporter PheP |
| RA | 603,208 | G→A | C417Y (TGC→TAC) | pheP → | phenylalanine:H(+) symporter PheP |
| RA | 615,848 | G→A | P564P (CCG→CCA) | entF → | apo‑serine activating enzyme |
| RA | 624,510 | C→T | M1M (GTG→ATG) † | fepB ← | ferric enterobactin ABC transporter periplasmic binding protein |
| RA | 631,633 | G→A | W580* (TGG→TGA) | cstA → | pyruvate transporter CstA |
| RA | 642,476 | G→A | S130N (AGT→AAT) | ybdR → | putative Zn(2(+))‑dependent alcohol dehydrogenase YbdR |
| RA | 668,829 | C→T | E70K (GAA→AAA) | rsfS ← | ribosomal silencing factor RsfS |
| RA | 675,108 | G→A | E31K (GAA→AAA) | ybeL → | DUF1451 domain‑containing protein YbeL |
| RA | 740,893 | G→A | A463T (GCA→ACA) | phr → | deoxyribodipyrimidine photolyase |
| RA | 793,557 | G→A | L78F (CTC→TTC) | modF ← | ABC family protein ModF |
| RA | 808,673 | G→A | A195A (GCC→GCT) | bioA ← | adenosylmethionine‑8‑amino‑7‑oxononanoate aminotransferase |
| RA | 817,297 | C→T | A85V (GCC→GTC) | moaA → | GTP 3',8'‑cyclase |
| RA | 846,078 | C→T | R129H (CGT→CAT) | glnQ ← | L‑glutamine ABC transporter ATP binding subunit |
| RA | 849,617 | C→T | A161T (GCT→ACT) | rhtA ← | L‑threonine/L‑homoserine exporter |
| RA | 862,786 | C→T | E242E (GAG→GAA) | ybiY ← | putative pyruvate formate‑lyase activating enzyme YbiY |
| RA | 987,152 | G→T | intergenic (‑170/+433) | ompF ← / ← asnS | outer membrane porin F/asparagine‑‑tRNA ligase |
| RA | 1,015,227 | G→A | S111N (AGC→AAC) | pqiC → | intermembrane transport lipoprotein PqiC |
| RA | 1,037,526 | G→A | A260T (GCA→ACA) | hyaF → | protein HyaF |
| RA | 1,065,815 | G→A | V77V (GTG→GTA) | agp → | glucose‑1‑phosphatase |
| RA | 1,077,066 | G→A | P606L (CCC→CTC) | putA ← | fused DNA‑binding transcriptional repressor/proline dehydrogenase/1‑pyrroline‑5‑carboxylate dehydrogenase PutA |
| RA | 1,077,466 | G→A | L473L (CTG→TTG) | putA ← | fused DNA‑binding transcriptional repressor/proline dehydrogenase/1‑pyrroline‑5‑carboxylate dehydrogenase PutA |
| JC JC | 1,105,376 | IS2 (–) +5 bp | intergenic (+83/‑34) | csgC → / → ymdA | curlin chaperone/uncharacterized protein YmdA |
| 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 | 1,196,277 | C→T | N385N (AAC→AAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,280 | G→C | A386A (GCG→GCC) | icd → | isocitrate dehydrogenase |
| RA | 1,196,283 | A→G | K387K (AAA→AAG) | icd → | isocitrate dehydrogenase |
| RA | 1,290,881 | C→T | L214F (CTT→TTT) | rssB → | regulator of RpoS |
| MC JC | 1,294,035 | Δ141 bp | [tdk] | [tdk] | |
| MC JC | 1,303,073 | Δ12 bp | coding (175‑186/921 nt) | oppB → | murein tripeptide ABC transporter/oligopeptide ABC transporter inner membrane subunit OppB |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,353,758 | T→A | D254V (GAT→GTT) | sapC ← | putrescine ABC exporter membrane protein SapC |
| RA | 1,412,163 | C→T | R358Q (CGG→CAG) | intR ← | putative integrase |
| RA | 1,412,294 | C→T | L314L (CTG→CTA) | intR ← | putative integrase |
| RA | 1,494,388 | Δ1 bp | coding (684/924 nt) | ydcI ← | DNA‑binding transcriptional dual regulator YdcI |
| RA | 1,517,508 | G→T | V40V (GTG→GTT) | ortT → | orphan toxin OrtT |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,667,887 | Δ1 bp | coding (678/1221 nt) | mlc ← | DNA‑binding transcriptional repressor Mlc |
| RA | 1,672,251 | G→A | V98M (GTG→ATG) | ydgD → | putative serine protease YdgD |
| RA | 1,680,659 | T→C | V368A (GTG→GCG) | ydgI → | putative arginine:ornithine antiporter |
| RA | 1,700,308 | C→T | R318R (CGC→CGT) | malX → | PTS enzyme IIBC component MalX |
| RA | 1,700,767 | C→T | C471C (TGC→TGT) | malX → | PTS enzyme IIBC component MalX |
| RA | 1,701,272 | C→T | Q106* (CAG→TAG) | malY → | negative regulator of MalT activity/cystathionine beta‑lyase |
| RA | 1,722,089 | G→A | G276S (GGC→AGC) | ydhJ → | putative membrane fusion protein YdhJ |
| RA | 1,744,751 | Δ1 bp | coding (1295/1374 nt) | mdtK → | multidrug efflux pump MdtK |
| RA | 1,750,270 | G→A | P27S (CCG→TCG) | ydhU ← | putative cytochrome YdhU |
| RA | 1,766,490 | G→A | F732F (TTC→TTT) | ydiJ ← | putative FAD‑linked oxidoreductase YdiJ |
| RA | 1,776,012 | G→A | G142G (GGG→GGA) | ydiF → | putative acetate‑CoA transferase YdiF |
| JC JC | 1,792,772 | IS2 (–) +5 bp | intergenic (‑41/+33) | nlpC ← / ← btuD | NlpC/P60 family lipoprotein NlpC/vitamin B12 ABC transporter ATP binding subunit |
| RA | 1,858,058 | A→G | M259T (ATG→ACG) | ydjJ ← | putative zinc‑binding dehydrogenase YdjJ |
| RA | 1,905,327 | C→T | intergenic (+68/‑361) | yobD → / → mntP | DUF986 domain‑containing inner membrane protein YobD/Mn(2(+)) exporter |
| RA | 1,936,057 | C→T | L86L (CTG→CTA) | zwf ← | NADP(+)‑dependent glucose‑6‑phosphate dehydrogenase |
| RA | 1,961,363 | C→T | L434L (CTC→CTT) | argS → | arginine‑‑tRNA ligase |
| RA | 1,978,243 | G→T | intergenic (‑46/+275) | flhD ← / ← insB5 | DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB |
| RA | 2,003,264 | C→T | E115K (GAA→AAA) | fliC ← | flagellar filament structural protein |
| RA | 2,007,727 | C→T | E122K (GAG→AAG) | yedD ← | lipoprotein YedD |
| RA | 2,032,423 | G→A | V219V (GTC→GTT) | yedJ ← | putative HD superfamily phosphohydrolase YedJ |
| RA | 2,077,829 | G→A | Q87Q (CAG→CAA) | cbtA → | cytoskeleton‑binding toxin CbtA |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| RA | 2,242,121 | A→G | S283P (TCG→CCG) | yeiB ← | DUF418 domain‑containing protein YeiB |
| JC JC | 2,269,876 | IS5 (+) +4 bp | intergenic (+309/‑100) | lpxT → / → mepS | lipid A‑core phosphotransferase/peptidoglycan endopeptidase/peptidoglycan L,D‑carboxypeptidase |
| JC JC | 2,319,850 | IS2 (+) +5 bp | coding (23‑27/2850 nt) | rcsC ← | histidine kinase RcsC |
| RA | 2,397,444 | G→A | Q908* (CAA→TAA) | nuoG ← | NADH:quinone oxidoreductase subunit G |
| JC JC | 2,406,780 | IS1 (–) +8 bp | intergenic (‑139/‑774) | lrhA ← / → alaA | DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA |
| MC JC | 2,558,699 | Δ6,790 bp | intZ–[eutA] | intZ, yffL, yffM, yffN, yffO, yffP, yffQ, yffR, yffS, [eutA] | |
| JC JC | 2,666,074 | IS1 (+) +9 bp | coding (640‑648/1281 nt) | csiE → | stationary phase‑inducible protein CsiE |
| RA | 3,268,970 | A→G | T186A (ACA→GCA) | yhaC → | uncharacterized protein YhaC |
| RA | 3,486,205 | C→A | T29K (ACG→AAG) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| MC JC | 3,682,261 | Δ34 bp | coding (1154‑1187/1287 nt) | dctA ← | C4 dicarboxylate/orotate:H(+) symporter |
| JC JC | 3,737,137 | IS2 (+) +5 bp | coding (37‑41/825 nt) | bax ← | putative glycoside hydrolase Bax |
| JC JC | 4,123,923 | IS2 (–) +5 bp | coding (530‑534/1026 nt) | cytR ← | DNA‑binding transcriptional repressor CytR |
| JC JC | 4,135,180 | IS2 (–) +5 bp | coding (1346‑1350/2181 nt) | katG → | catalase/hydroperoxidase HPI |
| RA | 4,146,389 | (T)6→7 | coding (132/879 nt) | pflC → | putative pyruvate formate‑lyase 2 activating enzyme PflC |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| JC JC | 4,536,236 | IS5 (+) +4 bp | intergenic (‑2183/‑358) | topAI ← / → ythB | toxin of the TopAI‑YjhQ toxin‑antitoxin system, TopA inhibitor/protein YthB |
| RA | 4,542,683 | Δ1 bp | intergenic (+50/‑432) | fimE → / → fimA | regulator for fimA/type 1 fimbriae major subunit |
| RA | 4,542,725 | (T)6→5 | intergenic (+92/‑390) | fimE → / → fimA | regulator for fimA/type 1 fimbriae major subunit |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196291 | 1211480 | 15190 | 6 [4] | [4] 6 | [icd]–mcrA | [icd],C0293,ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,ymfN,ymfR,beeE,ymfQ,ycfK,tfaP,tfaE,pinE,mcrA |
| * | * | ÷ | NC_000913 | 1978495 | 1979270 | 776 | 24 [0] | [0] 26 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 3423854–3424233 | 3424438–3424238 | 6–585 | 6 [5] | [5] 6 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 381260 = | NA (NA) | 33 (0.850) | 32/474 | 0.3 | NA | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382183 | NA (NA) | noncoding (924/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 382179 = | NA (NA) | 29 (0.750) | 29/470 | 0.4 | NA | noncoding (920/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382590 | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 566774 | 41 (1.060) | 13 (0.340) | 9/470 | 2.2 | 26.9% | pseudogene (91/93 nt) | renD | protein RenD |
| ? | NC_000913 | 568036 = | 30 (0.780) | pseudogene (2/213 nt) | renD | protein RenD | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 19 (0.500) | 18/466 | 1.1 | 100% | intergenic (+253/‑69) | ychE/insH21 | MarC family putative inner membrane protein YchE/IS5 family transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 24 (0.620) | 23/474 | 0.7 | 100% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1978494 | 0 (0.000) | intergenic (‑297/+24) | flhD/insB5 | DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB | |||||
| * | ? | NC_000913 | 1979271 = | 0 (0.000) | 26 (0.670) | 25/474 | 0.6 | 100% | intergenic (‑56/‑482) | insA5/uspC | IS1 family protein InsA/universal stress protein C |
| ? | NC_000913 | = 2102947 | NA (NA) | pseudogene (443/446 nt) | wbbL | interrupted rhamnosyltransferase WbbL | |||||