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 | seq id | position | mutation | freq | annotation | gene | description |
| RA | NZ_CP022686 | 238,324 | G→C | 18.0% | V85V (GTC→GTG) | sufE ← | cysteine desulfuration protein SufE |
| RA | NZ_CP022686 | 263,831 | A→C | 11.0% | intergenic (+38/+19) | fadK → / ← ppsA | medium‑chain fatty‑acid‑‑CoA ligase/phosphoenolpyruvate synthase |
| RA | NZ_CP022686 | 349,106 | A→C | 12.8% | T607P (ACC→CCC) | yeaG → | protein kinase YeaG |
| RA | NZ_CP022686 | 360,227 | T→G | 15.4% | T35P (ACG→CCG) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | NZ_CP022686 | 364,775 | C→A | 12.9% | E193* (GAA→TAA) | yeaY ← | Slp family lipoprotein YeaY |
| RA | NZ_CP022686 | 436,591 | A→C | 7.6% | intergenic (‑19/+38) | CIW80_RS02305 ← / ← CIW80_RS02310 | phage minor tail protein L/phage tail protein |
| RA | NZ_CP022686 | 457,894 | Δ1 bp | 100% | pseudogene (288/997 nt) | CIW80_RS02445 ← | DUF968 domain‑containing protein |
| RA | NZ_CP022686 | 560,880 | C→T | 100% | intergenic (+62/+53) | CIW80_RS03085 → / ← pilV | hypothetical protein/shufflon system plasmid conjugative transfer pilus tip adhesin PilV |
| RA | NZ_CP022686 | 576,323 | A→C | 8.5% | intergenic (+1/‑158) | CIW80_RS03170 → / → CIW80_RS03175 | DUF4756 family protein/H‑NS family nucleoid‑associated regulatory protein |
| RA | NZ_CP022686 | 601,295 | T→G | 17.2% | V1607G (GTC→GGC) | irp1 → | yersiniabactin polyketide synthase HMWP1 |
| MC JC | NZ_CP022686 | 628,478 | Δ1,286 bp | 100% | [clbP] | [clbP] | |
| RA | NZ_CP022686 | 636,757 | C→A | 14.4% | G438W (GGG→TGG) | clbM ← | precolibactin export MATE transporter ClbM |
| RA | NZ_CP022686 | 651,848 | A→C | 13.7% | R238R (CGT→CGG) | clbJ ← | colibactin non‑ribosomal peptide synthetase ClbJ |
| RA | NZ_CP022686 | 756,115 | A→G | 100% | G181G (GGT→GGC) | galE ← | UDP‑glucose 4‑epimerase GalE |
| RA | NZ_CP022686 | 764,997 | T→G | 13.1% | N41T (AAC→ACC) | wcaM ← | colanic acid biosynthesis protein WcaM |
| RA | NZ_CP022686 | 765,001 | A→T | 9.5% | Y40N (TAC→AAC) | wcaM ← | colanic acid biosynthesis protein WcaM |
| RA | NZ_CP022686 | 766,763 | A→T | 15.2% | Y288* (TAT→TAA) | wcaK ← | colanic acid biosynthesis pyruvyl transferase WcaK |
| RA | NZ_CP022686 | 794,460 | C→T | 100% | A568V (GCG→GTG) | dgcE → | diguanylate cyclase |
| RA | NZ_CP022686 | 829,441 | C→A | 33.8% | intergenic (‑30/+197) | gatY ← / ← fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| RA | NZ_CP022686 | 829,448 | T→A | 11.2% | intergenic (‑37/+190) | gatY ← / ← fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| RA | NZ_CP022686 | 829,452 | G→T | 24.2% | intergenic (‑41/+186) | gatY ← / ← fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| RA | NZ_CP022686 | 917,427:1 | +TT | 100% | intergenic (+130/‑91) | yeiP → / → yeiQ | elongation factor P‑like protein YeiP/mannitol dehydrogenase family protein |
| RA | NZ_CP022686 | 948,090 | C→A | 12.8% | intergenic (+159/‑98) | CIW80_RS04855 → / → CIW80_RS04860 | terminase small subunit/hypothetical protein |
| RA | NZ_CP022686 | 954,712 | T→G | 8.9% | Y134S (TAC→TCC) | ccmE ← | cytochrome c maturation protein CcmE |
| RA | NZ_CP022686 | 957,112 | T→G | 17.9% | T89P (ACC→CCC) | ccmA ← | cytochrome c biogenesis heme‑transporting ATPase CcmA |
| RA | NZ_CP022686 | 1,005,085 | C→A | 13.7% | T380T (ACC→ACA) | nrdA → | ribonucleoside‑diphosphate reductase subunit alpha |
| RA | NZ_CP022686 | 1,011,426 | G→C | 11.1% | M1M (ATG→ATC) † | glpA → | anaerobic glycerol‑3‑phosphate dehydrogenase subunit A |
| RA | NZ_CP022686 | 1,174,304 | A→T | 9.1% | intergenic (+33/‑11) | CIW80_RS05855 → / → CIW80_RS05860 | tRNA‑Val/tRNA‑Val |
| RA | NZ_CP022686 | 1,174,416 | A→T | 12.3% | intergenic (+26/‑21) | CIW80_RS05860 → / → CIW80_RS05865 | tRNA‑Val/tRNA‑Val |
| RA | NZ_CP022686 | 1,209,908 | T→G | 17.5% | D396A (GAC→GCC) | eutH ← | ethanolamine utilization protein EutH |
| RA | NZ_CP022686 | 1,360,709 | T→G | 8.3% | intergenic (‑44/+280) | kgtP ← / ← rrf | alpha‑ketoglutarate permease/5S ribosomal RNA |
| RA | NZ_CP022686 | 1,360,724 | G→T | 7.4% | intergenic (‑59/+265) | kgtP ← / ← rrf | alpha‑ketoglutarate permease/5S ribosomal RNA |
| RA | NZ_CP022686 | 1,424,198 | A→T | 8.7% | intergenic (‑34/+30) | CIW80_RS07080 ← / ← CIW80_RS07085 | tRNA‑Arg/tRNA‑Arg |
| RA | NZ_CP022686 | 1,479,607 | A→C | 8.8% | intergenic (‑16/+177) | ftsB ← / ← ygbE | cell division protein FtsB/DUF3561 family protein |
| RA | NZ_CP022686 | 1,504,308 | A→T | 12.1% | M249L (ATG→TTG) | CIW80_RS07520 → | YgcG family protein |
| RA | NZ_CP022686 | 1,546,996 | T→A | 14.8% | intergenic (+18/‑16) | CIW80_RS07705 → / → CIW80_RS07710 | tRNA‑Met/tRNA‑Met |
| RA | NZ_CP022686 | 1,547,000 | G→C | 11.9% | intergenic (+22/‑12) | CIW80_RS07705 → / → CIW80_RS07710 | tRNA‑Met/tRNA‑Met |
| RA | NZ_CP022686 | 1,547,110 | G→C | 22.9% | intergenic (+22/‑12) | CIW80_RS07710 → / → CIW80_RS07715 | tRNA‑Met/tRNA‑Met |
| RA | NZ_CP022686 | 1,564,573 | T→G | 11.0% | W192G (TGG→GGG) | CIW80_RS07780 → | ImcF‑related family protein |
| RA | NZ_CP022686 | 1,566,203 | A→C | 12.3% | N735T (AAC→ACC) | CIW80_RS07780 → | ImcF‑related family protein |
| RA | NZ_CP022686 | 1,674,224 | T→G | 16.9% | K188N (AAA→AAC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,674,231 | A→T | 11.7% | V186E (GTA→GAA) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,674,244 | T→G | 11.6% | T182P (ACC→CCC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,716,167 | A→C | 12.7% | N49T (AAC→ACC) | rdgB → | XTP/dITP diphosphatase |
| RA | NZ_CP022686 | 2,061,804 | A→C | 10.3% | K391N (AAA→AAC) | argG → | argininosuccinate synthase |
| RA | NZ_CP022686 | 2,110,465 | T→G | 8.2% | T10P (ACC→CCC) | rplM ← | 50S ribosomal protein L13 |
| RA | NZ_CP022686 | 2,130,829 | A→C | 9.9% | V237G (GTT→GGT) | mreC ← | rod shape‑determining protein MreC |
| RA | NZ_CP022686 | 2,148,103 | T→G | 18.0% | L122R (CTT→CGT) | panF → | sodium/pantothenate symporter |
| RA | NZ_CP022686 | 2,148,139 | C→G | 9.5% | A134G (GCG→GGG) | panF → | sodium/pantothenate symporter |
| RA | NZ_CP022686 | 2,185,075 | A→C | 8.1% | V46G (GTT→GGT) | rpsE ← | 30S ribosomal protein S5 |
| RA | NZ_CP022686 | 2,214,419 | T→C | 100% | K43R (AAA→AGA) | rpsL ← | 30S ribosomal protein S12 |
| RA | NZ_CP022686 | 2,305,978 | T→A | 9.1% | S220C (AGT→TGT) | CIW80_RS11625 ← | fimbrial biogenesis usher protein |
| RA | NZ_CP022686 | 2,320,775 | C→T | 100% | G274S (GGC→AGC) | CIW80_RS11675 ← | DNA‑processing protein DprA |
| RA | NZ_CP022686 | 2,361,489 | T→G | 19.2% | V188G (GTT→GGT) | nikA → | nickel ABC transporter substrate‑binding protein |
| RA | NZ_CP022686 | 2,393,013 | T→G | 5.7% | intergenic (+151/‑2) | slp → / → dctR | outer membrane lipoprotein Slp/LuxR C‑terminal‑related transcriptional regulator |
| RA | NZ_CP022686 | 2,408,861 | Δ1 bp | 100% | pseudogene (1097/3115 nt) | mdtF → | multidrug efflux pump RND permease MdtF |
| RA | NZ_CP022686 | 2,460,576 | C→A | 21.1% | M1M (ATG→ATT) † | yhjY ← | autotransporter outer membrane beta‑barrel domain‑containing protein |
| RA | NZ_CP022686 | 2,460,581 | A→C | 23.0% | intergenic (‑3/‑155) | yhjY ← / → tag | autotransporter outer membrane beta‑barrel domain‑containing protein/DNA‑3‑methyladenine glycosylase I |
| RA | NZ_CP022686 | 2,516,216 | T→C | 6.7% | S542S (TCT→TCC) | upaG → | trimeric autotransporter adhesin UpaG |
| RA | NZ_CP022686 | 2,516,873 | A→C | 10.2% | K761N (AAA→AAC) | upaG → | trimeric autotransporter adhesin UpaG |
| RA | NZ_CP022686 | 2,534,469 | A→C | 5.1% | V292G (GTC→GGC) | kbl ← | glycine C‑acetyltransferase |
| RA | NZ_CP022686 | 2,572,705 | A→C | 14.9% | G191G (GGT→GGG) | CIW80_RS12885 ← | ROK family protein |
| JC | NZ_CP022686 | 2,590,563 | +TTGG | 100% | coding (109/153 nt) | CIW80_RS26455 → | hypothetical protein |
| RA | NZ_CP022686 | 2,638,855 | C→A | 10.1% | intergenic (‑170/+70) | yidB ← / ← gyrB | YidB family protein/DNA topoisomerase (ATP‑hydrolyzing) subunit B |
| RA | NZ_CP022686 | 2,743,563 | T→G | 11.8% | noncoding (65/87 nt) | CIW80_RS13750 → | tRNA‑Leu |
| RA | NZ_CP022686 | 2,801,817 | T→G | 8.4% | Y32S (TAC→TCC) | CIW80_RS14030 ← | 2‑dehydro‑3‑deoxy‑6‑phosphogalactonate aldolase |
| RA | NZ_CP022686 | 2,868,740 | T→G | 21.0% | Q22P (CAG→CCG) | fdoH ← | formate dehydrogenase O subunit beta |
| RA | NZ_CP022686 | 2,904,856 | T→G | 7.2% | K237N (AAA→AAC) | ftsN ← | cell division protein FtsN |
| RA | NZ_CP022686 | 3,020,229 | T→G | 15.0% | V133G (GTC→GGC) | yjbB → | Na/Pi cotransporter family protein |
| RA | NZ_CP022686 | 3,080,461 | T→G | 11.0% | R158R (CGT→CGG) | CIW80_RS15320 → | Ldh family oxidoreductase |
| RA | NZ_CP022686 | 3,184,651 | A→C | 6.6% | intergenic (‑98/+18) | cutA ← / ← dcuA | divalent cation tolerance protein CutA/anaerobic C4‑dicarboxylate transporter DcuA |
| JC | NZ_CP022686 | 3,196,873 | +GCGTAATCGGTT | 100% | coding (944/1122 nt) | ampC ← | BlaEC family class C beta‑lactamase |
| RA | NZ_CP022686 | 3,265,084 | T→G | 16.5% | N77T (AAC→ACC) | ytfJ ← | YtfJ family protein |
| RA | NZ_CP022686 | 3,424,795 | A→C | 100% | intergenic (‑41/+27) | yjiJ ← / ← yjiK | MFS transporter/YjiK family protein |
| RA | NZ_CP022686 | 3,461,199 | T→G | 17.2% | intergenic (‑8/+27) | CIW80_RS17335 ← / ← CIW80_RS17340 | tRNA‑Leu/tRNA‑Leu |
| RA | NZ_CP022686 | 3,461,218 | G→C | 14.0% | intergenic (‑27/+8) | CIW80_RS17335 ← / ← CIW80_RS17340 | tRNA‑Leu/tRNA‑Leu |
| RA | NZ_CP022686 | 3,461,229 | T→G | 14.7% | noncoding (84/87 nt) | CIW80_RS17340 ← | tRNA‑Leu |
| MC JC | NZ_CP022686 | 3,559,837 | Δ2,343 bp | 100% | coding (10‑2352/2352 nt) | polB ← | DNA polymerase II |
| RA | NZ_CP022686 | 3,652,079 | T→G | 11.9% | intergenic (‑88/+24) | panB ← / ← CIW80_RS18255 | 3‑methyl‑2‑oxobutanoate hydroxymethyltransferase/fimbrial‑like adhesin |
| RA | NZ_CP022686 | 3,656,188 | A→G | 100% | S549P (TCC→CCC) | htrE ← | outer membrane usher protein |
| RA | NZ_CP022686 | 3,703,648 | A→C | 6.9% | T120P (ACG→CCG) | fabZ → | 3‑hydroxyacyl‑ACP dehydratase FabZ |
| RA | NZ_CP022686 | 3,792,805 | A→G | 100% | Y421C (TAC→TGC) | fucP → | L‑fucose:H+ symporter permease |
| MC JC | NZ_CP022686 | 3,844,426 | Δ1,036 bp | 100% | coding (2‑1037/1056 nt) | dinB → | DNA polymerase IV |
| RA | NZ_CP022686 | 3,852,459 | T→G | 10.1% | N178T (AAC→ACC) | phoE ← | phosphoporin PhoE |
| RA | NZ_CP022686 | 3,928,345 | T→G | 10.1% | F277V (TTC→GTC) | prpE → | propionate‑‑CoA ligase |
| RA | NZ_CP022686 | 3,928,369 | T→G | 11.4% | W285G (TGG→GGG) | prpE → | propionate‑‑CoA ligase |
| RA | NZ_CP022686 | 3,935,324 | T→G | 13.1% | N705T (AAC→ACC) | lacZ ← | beta‑galactosidase |
| RA | NZ_CP022686 | 3,981,933 | T→G | 10.4% | intergenic (+70/‑86) | proY → / → malZ | proline‑specific permease ProY/maltodextrin glucosidase |
| RA | NZ_CP022686 | 4,014,242 | A→T | 16.1% | intergenic (+88/‑256) | bolA → / → tig | transcriptional regulator BolA/trigger factor |
| RA | NZ_CP022686 | 4,014,248 | C→G | 12.4% | intergenic (+94/‑250) | bolA → / → tig | transcriptional regulator BolA/trigger factor |
| RA | NZ_CP022686 | 4,032,292 | A→C | 17.9% | E106D (GAA→GAC) | glnK → | P‑II family nitrogen regulator |
| RA | NZ_CP022686 | 4,151,277 | T→G | 6.9% | T73P (ACC→CCC) | fepB ← | Fe2+‑enterobactin ABC transporter substrate‑binding protein |
| RA | NZ_CP022686 | 4,196,276 | T→G | 16.5% | E15D (GAA→GAC) | holA ← | DNA polymerase III subunit delta |
| RA | NZ_CP022686 | 4,214,235 | C→A | 7.0% | intergenic (‑23/+26) | CIW80_RS21085 ← / ← CIW80_RS21090 | tRNA‑Gln/tRNA‑Met |
| RA | NZ_CP022686 | 4,280,091 | T→G | 7.9% | V102G (GTC→GGC) | cydB → | cytochrome d ubiquinol oxidase subunit II |
| RA | NZ_CP022686 | 4,301,920 | T→G | 11.0% | V136G (GTT→GGT) | modB → | molybdate ABC transporter permease subunit |
| RA | NZ_CP022686 | 4,331,929 | C→A | 17.0% | M292I (ATG→ATT) | ybhR ← | ABC transporter permease |
| RA | NZ_CP022686 | 4,368,341 | T→G | 13.1% | D47A (GAC→GCC) | ybiY ← | glycyl‑radical enzyme activating protein |
| RA | NZ_CP022686 | 4,368,380 | T→G | 10.6% | N34T (AAC→ACC) | ybiY ← | glycyl‑radical enzyme activating protein |
| RA | NZ_CP022686 | 4,440,334 | A→G | 11.2% | Q797Q (CAA→CAG) | ftsK → | DNA translocase FtsK |
| RA | NZ_CP022686 | 4,485,614 | T→G | 9.9% | F139V (TTT→GTT) | gloC → | hydroxyacylglutathione hydrolase GloC |
| RA | NZ_CP022686 | 4,605,579 | T→G | 17.8% | T56P (ACG→CCG) | CIW80_RS23010 ← | hypothetical protein |
| RA | NZ_CP022686 | 4,632,182 | T→G | 10.1% | R276R (CGT→CGG) | mchF → | microcin export transporter peptidase/ATP‑binding subunit MchF |
| RA | NZ_CP022686 | 4,642,951 | A→C | 10.6% | N732T (AAC→ACC) | sfaF → | S/F1C fimbrial usher SfaF/FocD |
| RA | NZ_CP022686 | 4,678,047 | A→C | 24.5% | intergenic (+45/‑76) | agn43 → / → CIW80_RS23450 | autotransporter adhesin Ag43/hypothetical protein |
| RA | NZ_CP022686 | 4,764,877 | T→G | 15.5% | intergenic (‑57/‑204) | ycfT ← / → lolC | acyltransferase family protein/lipoprotein‑releasing ABC transporter permease subunit LolC |
| RA | NZ_CP022686 | 4,764,880 | T→G | 11.6% | intergenic (‑60/‑201) | ycfT ← / → lolC | acyltransferase family protein/lipoprotein‑releasing ABC transporter permease subunit LolC |
| RA | NZ_CP022686 | 4,764,883 | A→T | 9.0% | intergenic (‑63/‑198) | ycfT ← / → lolC | acyltransferase family protein/lipoprotein‑releasing ABC transporter permease subunit LolC |
| RA | NZ_CP022686 | 4,780,176 | A→C | 17.0% | intergenic (‑75/+95) | phoP ← / ← purB | two‑component system response regulator PhoP/adenylosuccinate lyase |
| RA | NZ_CP022686 | 4,809,437 | T→G | 7.7% | L49R (CTG→CGG) | CIW80_RS24260 → | head‑tail joining protein |
| RA | NZ_CP022686 | 4,809,441 | T→G | 12.3% | G50G (GGT→GGG) | CIW80_RS24260 → | head‑tail joining protein |
| MC JC | NZ_CP022686 | 4,844,868 | Δ1,662 bp | 100% | [umuD]–[umuC] | [umuD], [umuC] | |
| RA | NZ_CP022686 | 4,870,912 | Δ1 bp | 100% | intergenic (‑108/‑120) | dhaK ← / → dhaR | dihydroxyacetone kinase subunit DhaK/dihydroxyacetone kinase operon transcriptional regulator DhaR |
| RA | NZ_CP022686 | 4,909,051 | A→C | 13.0% | noncoding (53/132 nt) | CIW80_RS24835 ← | RtT sRNA |
| RA | NZ_CP022686 | 4,918,837 | T→G | 5.9% | K390N (AAA→AAC) | adhE ← | bifunctional acetaldehyde‑CoA/alcohol dehydrogenase |
| RA | NZ_CP022686 | 4,945,322 | G→T | 7.7% | D72Y (GAT→TAT) | yciQ → | DUF2207 domain‑containing protein |
| RA | NZ_CP022686 | 4,951,521 | A→C | 11.3% | T39P (ACC→CCC) | topA → | type I DNA topoisomerase |
| RA | NZ_CP022686 | 5,000,015 | T→G | 9.8% | F156V (TTT→GTT) | CIW80_RS25310 → | ABC transporter ATP‑binding protein |
| RA | NZ_CP022686 | 5,001,164 | A→C | 12.3% | N163T (AAC→ACC) | ompG → | monomeric porin OmpG |
| RA | NZ_CP022686 | 5,042,304 | T→C | 7.9% | N645N (AAT→AAC) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | pMut‑Ompa‑D5‑IL2wt‑His6 | 2,031 | G→A | 100% | intergenic (‑235/‑1500) | putative rom (RNA I inhibition modulator protein) ← / → ompA | –/– |
| JC | pMut‑Ompa‑D5‑IL2wt‑His6 | 3,595 | Δ15 bp | 100% | [IL2wt no signal] | [IL2wt no signal] | |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NZ_MW240712 | 188–2618 | 3086–2957 | 340–2899 | 8568 [8322] | [8341] 8885 | JNG15_RS00005–mobA | JNG15_RS00005,JNG15_RS00010,JNG15_RS00015,mobA |
| * | * | ÷ | pMut‑Ompa‑D5‑IL2wt‑His6 | 4749–4809 | 5478–5073 | 265–730 | 3695 [3679] | [0] NA | [putative HTH domain protein] | [putative HTH domain protein] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP022686 | 262466 = | 4 (0.020) | 189 (1.140) | 69/248 | NT | 97.9% | coding (320/1647 nt) | fadK | medium‑chain fatty‑acid‑‑CoA ligase |
| ? | NZ_CP022686 | = 1524130 | NA (NA) | intergenic (+8/+232) | CIW80_RS07590/syd | IS3‑like element ISEc52 family transposase/SecY‑interacting protein | |||||
| * | ? | NZ_CP022686 | = 262468 | 3 (0.020) | 133 (0.800) | 61/248 | NT | 97.8% | coding (322/1647 nt) | fadK | medium‑chain fatty‑acid‑‑CoA ligase |
| ? | NZ_CP022686 | = 1761697 | NA (NA) | intergenic (‑72/‑70) | CIW80_RS08710/CIW80_RS08720 | IS3‑like element ISEc52 family transposase/IS3‑like element IS600 family transposase | |||||