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 | 19,273 | G→T | A187S (GCT→TCT) | nhaR → | DNA‑binding transcriptional activator NhaR |
| RA | 117,261 | G→T | Q97K (CAA→AAA) | ppdD ← | prepilin peptidase‑dependent protein |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 294,306 | T→C | N165S (AAT→AGT) | yagM ← | CP4‑6 prophage; protein YagM |
| RA | 335,858 | G→T | A193A (GCG→GCT) | yahD → | ankyrin repeat‑containing protein YahD |
| RA | 398,030 | C→A | R53R (CGC→CGA) | yaiW → | surface‑exposed outer membrane lipoprotein |
| RA | 577,334 | C→A | intergenic (‑509/‑64) | nmpC ← / → essD | DLP12 prophage; putative outer membrane porin NmpC/DLP12 prophage; putative phage lysis protein |
| RA | 587,517 | G→A | A155A (GCC→GCT) | ybcH ← | DUF4434 domain‑containing protein YbcH |
| RA | 620,013 | G→T | H63N (CAT→AAT) | fepC ← | ferric enterobactin ABC transporter ATP binding subunit |
| RA | 637,080 | C→A | R180M (AGG→ATG) | ybdO ← | putative LysR family DNA‑binding transcriptional regulator YbdO |
| RA | 679,202 | G→T | L69I (CTT→ATT) | ybeT ← | Sel1 repeat‑containing protein YbeT |
| RA | 724,088 | G→T | D109E (GAC→GAA) | kdpD ← | sensory histidine kinase KdpD |
| RA | 796,750 | A→T | E66V (GAA→GTA) | modC → | molybdate ABC transporter ATP binding subunit |
| RA | 812,628 | G→T | G120V (GGC→GTC) | bioD → | dethiobiotin synthetase |
| RA | 854,043 | G→T | A133S (GCT→TCT) | ybiR → | putative transporter YbiR |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 903,928 | G→T | intergenic (‑194/+24) | artP ← / ← ybjP | L‑arginine ABC transporter ATP binding subunit/DUF3828 domain‑containing lipoprotein YbjP |
| RA | 908,944 | C→A | A117A (GCG→GCT) | ltaE ← | low‑specificity L‑threonine aldolase |
| RA | 1,112,234 | C→A | R458S (CGT→AGT) | opgH → | osmoregulated periplasmic glucans (OPGs) biosynthesis protein H |
| 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 | 1,299,045 | C→A | L150M (CTG→ATG) | ychE → | putative inner membrane protein |
| RA | 1,312,266 | Δ1 bp | intergenic (‑20/+85) | yciA ← / ← yciB | acyl‑CoA thioesterase/inner membrane protein |
| RA | 1,330,298 | G→T | D323Y (GAC→TAC) | sohB → | S49 peptidase family protein |
| RA | 1,537,475 | G→T | T460N (ACC→AAC) | narY ← | nitrate reductase Z subunit beta |
| RA | 1,561,966 | A→G | N172N (AAT→AAC) | ddpA ← | putative D,D‑dipeptide ABC transporter periplasmic binding protein |
| JC JC | 1,588,441 | IS2 (–) +5 bp | coding (395‑399/531 nt) | ydeS ← | putative fimbrial protein YdeS |
| RA | 1,678,604 | G→T | A60S (GCA→TCA) | ydgH → | DUF1471 domain‑containing protein YdgH |
| RA | 1,696,029 | G→T | L15I (CTC→ATC) | uidA ← | beta‑glucuronidase |
| RA | 1,713,501 | G→T | A245S (GCG→TCG) | dtpA → | dipeptide/tripeptide:H(+) symporter DtpA |
| RA | 1,746,447 | C→A | noncoding (13/77 nt) | valV → | tRNA‑Val |
| RA | 1,748,080 | G→T | W317L (TGG→TTG) | ydhS → | FAD/NAD(P) binding domain‑containing protein YdhS |
| RA | 1,818,556 | T→A | intergenic (‑56/+49) | chbF ← / ← chbR | monoacetylchitobiose‑6‑phosphate hydrolase/DNA‑binding transcriptional dual regulator ChbR |
| RA | 1,836,690 | C→A | P206P (CCC→CCA) | ynjB → | putative ABC transporter periplasmic binding protein YnjB |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,963,377 | G→T | L558L (CTC→CTA) | flhA ← | flagellar biosynthesis protein FlhA |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 1,992,911 | C→T | G599D (GGT→GAT) | uvrC ← | excision nuclease subunit C |
| RA | 2,096,718 | C→A | G35G (GGC→GGA) | hisI → | putative bifunctional phosphoribosyl‑AMP cyclohydrolase/phosphoribosyl‑ATP pyrophosphatase |
| RA | 2,134,818 | C→T | V279I (GTA→ATA) | wzc ← | protein‑tyrosine kinase Wzc |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,452,929 | G→T | pseudogene (2073/2646 nt) | yfcU ← | putative outer membrane usher protein YfcU |
| RA | 2,503,854 | G→T | A211E (GCG→GAG) | fryA ← | putative PTS multiphosphoryl transfer protein FryA |
| RA | 2,564,920 | C→T | P133L (CCA→CTA) | yffS → | CPZ‑55 prophage; uncharacterized protein YffS |
| RA | 2,588,322 | C→A | P243Q (CCA→CAA) | acrD → | multidrug efflux pump RND permease AcrD |
| RA | 2,626,466 | C→A | A451E (GCA→GAA) | ppx → | exopolyphosphatase |
| RA | 2,847,755 | G→C | T496S (ACC→AGC) | hycC ← | formate hydrogenlyase subunit HycC |
| RA | 2,960,200 | G→T | F743L (TTC→TTA) | recC ← | exodeoxyribonuclease V subunit RecC |
| RA | 3,144,577 | G→T | G188G (GGC→GGA) | hybA ← | hydrogenase 2 iron‑sulfur protein |
| RA | 3,145,058 | G→T | A28D (GCT→GAT) | hybA ← | hydrogenase 2 iron‑sulfur protein |
| RA | 3,184,853 | A→G | K5R (AAA→AGA) | ubiK → | ubiquinone biosynthesis accessory factor UbiK |
| RA | 3,207,015 | C→A | L185I (CTC→ATC) | ttdA → | L(+)‑tartrate dehydratase subunit alpha |
| RA | 3,305,861 | G→T | intergenic (‑44/+110) | mtr ← / ← deaD | tryptophan:H(+) symporter Mtr/ATP‑dependent RNA helicase DeaD |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,394,310 | G→T | A650E (GCG→GAG) | yhdP ← | AsmA2 domain‑containing protein |
| RA | 3,447,015 | C→A | D142Y (GAC→TAC) | rplE ← | 50S ribosomal subunit protein L5 |
| RA | 3,451,751 | C→A | S179I (AGC→ATC) | rplD ← | 50S ribosomal subunit protein L4 |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,629,955 | G→T | A216A (GCC→GCA) | yhiI ← | putative membrane fusion protein YhiI |
| RA | 3,673,711 | C→A | P117Q (CCG→CAG) | yhjD → | putative transporter YhjD |
| RA | 3,688,775 | C→A | A133A (GCG→GCT) | bcsC ← | cellulose biosynthesis protein BcsC |
| RA | 3,749,430 | G→T | V67F (GTT→TTT) | sgbU → | putative L‑xylulose 5‑phosphate 3‑epimerase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,895,005 | G→T | M118I (ATG→ATT) | yieF → | chromate reductase |
| RA | 3,938,138 | C→A | A282D (GCT→GAT) | rbsK → | ribokinase |
| RA | 3,938,946 | G→A | Q240Q (CAG→CAA) | rbsR → | DNA‑binding transcriptional dual regulator RbsR |
| RA | 3,946,604 | C→A | noncoding (2901/2904 nt) | rrlC → | 23S ribosomal RNA |
| RA | 3,967,531 | C→A | T372K (ACG→AAG) | rho → | transcription termination factor Rho |
| RA | 4,015,884 | C→T | G96S (GGC→AGC) | ysgA ← | putative dienelactone hydrolase |
| RA | 4,261,710 | C→A | S14R (AGC→AGA) | dusA → | tRNA‑dihydrouridine synthase A |
| RA | 4,286,408 | C→A | A322S (GCC→TCC) | acs ← | acetyl‑CoA synthetase (AMP‑forming) |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,392,304 | C→A | intergenic (+155/‑56) | orn → / → glyV | oligoribonuclease/tRNA‑Gly |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196254 | 1211437 | 15184 | 45 [41] | [40] 43 | [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 | 3102954 | 3104072 | 1119 | 43 [42] | [41] 43 | mutY | mutY |
| * | * | ÷ | NC_000913 | 3423768–3424234 | 3424531–3424238 | 5–764 | 43 [41] | [38] 43 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 155 (1.120) | 81/270 | 0.1 | 100% | intergenic (+253/‑33) | ychE/insH21 | putative inner membrane protein/IS5 transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 3363001 = | 223 (1.570) | 245 (1.740) | 84/276 | 0.1 | 68.6% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 3 (0.020) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 179 (1.260) | 83/278 | 0.1 | 97.3% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 5 (0.040) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||