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 | 138,874 | G→A | D784D (GAC→GAT) | gcd ← | quinoprotein glucose dehydrogenase |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 349,528 | G→A | E283K (GAA→AAA) | prpB → | 2‑methylisocitrate lyase |
| RA | 528,086 | G→A | intergenic (+137/+1559) | ybbC → / ← ylbG | PF15631 family protein YbbC/putative DNA‑binding transcriptional regulator YlbG |
| 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 | 631,633 | G→A | W580* (TGG→TGA) | cstA → | pyruvate transporter CstA |
| RA | 648,499 | C→T | G358D (GGC→GAC) | citF ← | citrate lyase alpha subunit |
| RA | 691,560 | G→A | P75P (CCC→CCT) | ybeX ← | CorC‑HlyC family protein YbeX |
| RA | 987,152 | G→T | intergenic (‑170/+433) | ompF ← / ← asnS | outer membrane porin F/asparagine‑‑tRNA ligase |
| RA | 988,339 | C→T | G216D (GGC→GAC) | asnS ← | asparagine‑‑tRNA ligase |
| RA | 1,012,634 | C→T | P212S (CCA→TCA) | pqiA → | intermembrane transport protein PqiA |
| RA | 1,028,235 | C→T | T97I (ACT→ATT) | yccU → | putative HspQ acetyl donor |
| JC JC | 1,105,376 | IS2 (–) +5 bp | intergenic (+83/‑34) | csgC → / → ymdA | curlin chaperone/uncharacterized protein YmdA |
| RA | 1,136,015 | C→T | T151M (ACG→ATG) | flgH → | flagellar L‑ring protein |
| 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 | 1,196,292 | C→T | T390T (ACC→ACT) | 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 | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| 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 | 1,427,946 | C→T | A261T (GCC→ACC) | insH5 ← | IS5 family transposase and trans‑activator |
| RA | 1,428,052 | T→C | G225G (GGA→GGG) | insH5 ← | IS5 family transposase and trans‑activator |
| 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 | 1,744,751 | Δ1 bp | coding (1295/1374 nt) | mdtK → | multidrug efflux pump MdtK |
| 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 | 1,879,287 | G→A | intergenic (‑32/+116) | yeaQ ← / ← yoaG | PF04226 family protein YeaQ/DUF1869 domain‑containing protein YoaG |
| RA | 1,939,533 | C→T | D221N (GAT→AAT) | lpxM ← | Lipid A biosynthesis myristoyltransferase |
| 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 | 2,032,423 | G→A | V219V (GTC→GTT) | yedJ ← | putative HD superfamily phosphohydrolase YedJ |
| 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 |
| RA | 2,269,958 | C→T | intergenic (+391/‑21) | 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 | 2,919,584 | T→C | K388R (AAA→AGA) | gudX ← | glucarate dehydratase‑related protein |
| RA | 2,924,332 | G→A | noncoding (193/369 nt) | csrB ← | small regulatory RNA CsrB |
| RA | 3,143,919 | C→T | G82G (GGG→GGA) | hybB ← | hydrogenase 2 membrane subunit |
| RA | 3,180,123 | C→T | A127V (GCC→GTC) | ygiB → | DUF1190 domain‑containing protein YgiB |
| RA | 3,225,414 | G→A | V928I (GTT→ATT) | ebgA → | evolved beta‑D‑galactosidase subunit alpha |
| RA | 3,229,511 | G→A | W208* (TGG→TGA) | ygjK → | glycoside hydrolase |
| RA | 3,229,588 | G→A | R234H (CGC→CAC) | ygjK → | glycoside hydrolase |
| RA | 3,232,686 | C→T | A341V (GCC→GTC) | fadH → | 2,4‑dienoyl‑CoA reductase |
| RA | 3,233,317 | C→T | I551I (ATC→ATT) | fadH → | 2,4‑dienoyl‑CoA reductase |
| RA | 3,268,970 | A→G | T186A (ACA→GCA) | yhaC → | uncharacterized protein YhaC |
| JC JC | 3,291,527 | IS2 (–) +5 bp | coding (187‑191/1092 nt) | yraK → | putative fimbrial adhesin YraK |
| 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 |
| RA | 3,646,711 | C→T | A138V (GCC→GTC) | gor → | glutathione reductase (NADPH) |
| MC JC | 3,682,261 | Δ34 bp | coding (1154‑1187/1287 nt) | dctA ← | C4 dicarboxylate/orotate:H(+) symporter |
| RA | 3,682,511 | C→T | A313T (GCG→ACG) | dctA ← | C4 dicarboxylate/orotate:H(+) symporter |
| JC JC | 3,737,137 | IS2 (+) +5 bp | coding (37‑41/825 nt) | bax ← | putative glycoside hydrolase Bax |
| RA | 3,947,919 | G→A | H17Y (CAC→TAC) | hdfR ← | DNA‑binding transcriptional dual regulator HdfR |
| 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 | 4,136,115 | C→T | A3V (GCC→GTC) | yijE → | cystine exporter |
| RA | 4,146,389 | (T)6→7 | coding (132/879 nt) | pflC → | putative pyruvate formate‑lyase 2 activating enzyme PflC |
| RA | 4,236,235 | G→A | intergenic (+87/‑27) | yjbE → / → yjbF | uncharacterized protein YjbE/lipoprotein YjbF |
| 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 |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196304 | 1211470 | 15167 | 31 [29] | [30] 31 | [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 | 88 [0] | [0] 129 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 3423799–3424233 | 3424492–3424239 | 7–694 | 31 [30] | [30] 33 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 381260 = | NA (NA) | 76 (0.860) | 46/598 | 0.7 | 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) | 33 (0.380) | 27/594 | 2.4 | NA | noncoding (920/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382590 | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 88 (0.990) | 63/598 | 0.2 | 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) | 129 (1.460) | 86/598 | 0.0 | 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 | |||||