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 | 360,227 | T→G | 20.1% | T35P (ACG→CCG) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | NZ_CP022686 | 457,894 | Δ1 bp | 100% | pseudogene (288/997 nt) | CIW80_RS02445 ← | DUF968 domain‑containing protein |
| RA | NZ_CP022686 | 556,948 | A→T | 16.7% | intergenic (+132/‑716) | zinT → / → CIW80_RS03080 | metal‑binding protein ZinT/site‑specific integrase |
| 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 | 601,302 | T→G | 19.0% | R1609R (CGT→CGG) | irp1 → | yersiniabactin polyketide synthase HMWP1 |
| MC JC | NZ_CP022686 | 628,478 | Δ1,286 bp | 100% | [clbP] | [clbP] | |
| RA | NZ_CP022686 | 756,115 | A→G | 100% | G181G (GGT→GGC) | galE ← | UDP‑glucose 4‑epimerase GalE |
| RA | NZ_CP022686 | 794,460 | C→T | 100% | A568V (GCG→GTG) | dgcE → | diguanylate cyclase |
| 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 | 937,864 | G→A | 100% | G29R (GGA→AGA) | CIW80_RS04770 → | integrase domain‑containing protein |
| RA | NZ_CP022686 | 948,090 | C→A | 12.2% | intergenic (+159/‑98) | CIW80_RS04855 → / → CIW80_RS04860 | terminase small subunit/hypothetical protein |
| JC | NZ_CP022686 | 1,061,329 | Δ6 bp | 5.3% | coding (42‑47/945 nt) | lrhA ← | transcriptional regulator LrhA |
| RA | NZ_CP022686 | 1,065,997 | A→C | 11.6% | A30A (GCT→GCG) | yfbS ← | SLC13 family permease |
| RA | NZ_CP022686 | 1,145,570 | C→G | 13.3% | L333F (TTG→TTC) | oxc ← | oxalyl‑CoA decarboxylase |
| RA | NZ_CP022686 | 1,174,272 | A→C | 12.6% | intergenic (+1/‑43) | CIW80_RS05855 → / → CIW80_RS05860 | tRNA‑Val/tRNA‑Val |
| RA | NZ_CP022686 | 1,174,279 | A→T | 7.1% | intergenic (+8/‑36) | CIW80_RS05855 → / → CIW80_RS05860 | tRNA‑Val/tRNA‑Val |
| RA | NZ_CP022686 | 1,209,908 | T→G | 15.7% | D396A (GAC→GCC) | eutH ← | ethanolamine utilization protein EutH |
| RA | NZ_CP022686 | 1,213,479 | T→G | 14.8% | G420G (GGA→GGC) | eutE ← | aldehyde dehydrogenase EutE |
| RA | NZ_CP022686 | 1,239,833 | G→T | 18.3% | intergenic (‑130/+38) | ypfJ ← / ← purC | neutral zinc metallopeptidase/phosphoribosylaminoimidazolesuccinocarboxamide synthase |
| RA | NZ_CP022686 | 1,504,361 | G→T | 23.1% | V266V (GTG→GTT) | CIW80_RS07520 → | YgcG family protein |
| RA | NZ_CP022686 | 1,632,501 | T→G | 10.8% | V166G (GTT→GGT) | arcC → | carbamate kinase |
| RA | NZ_CP022686 | 1,633,846 | T→G | 30.1% | N253T (AAC→ACC) | yqeB ← | selenium‑dependent molybdenum cofactor biosynthesis protein YqeB |
| RA | NZ_CP022686 | 1,640,925 | A→C | 18.6% | R7S (AGA→AGC) | ygfM → | molybdopterin‑dependent oxidoreductase FAD‑binding subunit |
| RA | NZ_CP022686 | 1,674,224 | T→G | 15.4% | K188N (AAA→AAC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,674,231 | A→T | 14.6% | V186E (GTA→GAA) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,674,244 | T→G | 13.7% | T182P (ACC→CCC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,706,047 | G→T | 12.6% | M1M (ATG→ATT) † | metK → | methionine adenosyltransferase |
| RA | NZ_CP022686 | 1,745,268 | A→C | 10.8% | L183R (CTG→CGG) | CIW80_RS08660 ← | MFS transporter |
| RA | NZ_CP022686 | 1,805,056 | A→C | 12.0% | pseudogene (337/934 nt) | CIW80_RS09020 → | nucleotidyl transferase AbiEii/AbiGii toxin family protein |
| RA | NZ_CP022686 | 1,828,113 | A→C | 11.0% | P84P (CCT→CCG) | gspK ← | type II secretion system minor pseudopilin GspK |
| RA | NZ_CP022686 | 1,965,173 | A→C | 11.3% | R86R (CGT→CGG) | nfeF ← | NADPH‑dependent ferric chelate reductase |
| RA | NZ_CP022686 | 2,016,170 | A→C | 11.0% | noncoding (104/377 nt) | rnpB ← | RNase P RNA component class A |
| RA | NZ_CP022686 | 2,037,521 | A→C | 12.6% | T508P (ACC→CCC) | lpoA → | penicillin‑binding protein activator LpoA |
| RA | NZ_CP022686 | 2,049,089 | T→G | 17.4% | N256T (AAC→ACC) | deaD ← | ATP‑dependent RNA helicase DeaD |
| RA | NZ_CP022686 | 2,056,168 | A→C | 9.4% | G614G (GGT→GGG) | infB ← | translation initiation factor IF‑2 |
| RA | NZ_CP022686 | 2,130,829 | A→C | 7.7% | V237G (GTT→GGT) | mreC ← | rod shape‑determining protein MreC |
| RA | NZ_CP022686 | 2,148,132 | C→G | 12.9% | L132V (CTG→GTG) | panF → | sodium/pantothenate symporter |
| RA | NZ_CP022686 | 2,148,141 | T→G | 11.9% | F135V (TTC→GTC) | panF → | sodium/pantothenate symporter |
| RA | NZ_CP022686 | 2,172,177 | A→C | 8.4% | G87G (GGT→GGG) | smg ← | DUF494 family protein Smg |
| RA | NZ_CP022686 | 2,179,878 | T→G | 10.9% | K35T (AAG→ACG) | rplQ ← | 50S ribosomal protein L17 |
| RA | NZ_CP022686 | 2,214,419 | T→C | 100% | K43R (AAA→AGA) | rpsL ← | 30S ribosomal protein S12 |
| RA | NZ_CP022686 | 2,250,454 | A→C | 7.0% | S40A (TCG→GCG) | dam ← | adenine‑specific DNA‑methyltransferase |
| RA | NZ_CP022686 | 2,272,831 | G→T | 9.8% | intergenic (+73/‑24) | greB → / → yhgF | transcription elongation factor GreB/Tex family protein |
| RA | NZ_CP022686 | 2,320,775 | C→T | 100% | G274S (GGC→AGC) | CIW80_RS11675 ← | DNA‑processing protein DprA |
| RA | NZ_CP022686 | 2,357,324 | A→C | 20.1% | N37T (AAC→ACC) | dcrB → | phage sensitivity protein DcrB |
| RA | NZ_CP022686 | 2,394,287 | T→G | 18.8% | N115T (AAC→ACC) | chuS ← | hematinate‑forming heme oxygenase ChuS |
| RA | NZ_CP022686 | 2,408,861 | Δ1 bp | 100% | pseudogene (1097/3115 nt) | mdtF → | multidrug efflux pump RND permease MdtF |
| RA | NZ_CP022686 | 2,447,824 | G→T | 6.3% | L26M (CTG→ATG) | CIW80_RS12290 ← | type I toxin‑antitoxin system toxin Ldr family protein |
| RA | NZ_CP022686 | 2,460,581 | A→C | 24.2% | intergenic (‑3/‑155) | yhjY ← / → tag | autotransporter outer membrane beta‑barrel domain‑containing protein/DNA‑3‑methyladenine glycosylase I |
| RA | NZ_CP022686 | 2,546,394 | A→C | 13.1% | V95G (GTT→GGT) | waaG ← | glycosyltransferase family 4 protein |
| RA | NZ_CP022686 | 2,546,400 | A→C | 17.9% | L93R (CTG→CGG) | waaG ← | glycosyltransferase family 4 protein |
| RA | NZ_CP022686 | 2,558,864 | T→G | 9.4% | F128V (TTT→GTT) | yicG → | trimeric intracellular cation channel family protein |
| JC | NZ_CP022686 | 2,590,563 | +TTGG | 100% | coding (109/153 nt) | CIW80_RS26455 → | hypothetical protein |
| RA | NZ_CP022686 | 2,616,198 | G→T | 59.4% | G260C (GGT→TGT) | CIW80_RS13115 → | hypothetical protein |
| RA | NZ_CP022686 | 2,736,585 | T→A | 7.9% | Y183N (TAC→AAC) | rffA → | dTDP‑4‑amino‑4,6‑dideoxygalactose transaminase |
| RA | NZ_CP022686 | 2,834,886 | A→C | 9.0% | K597N (AAA→AAC) | polA → | DNA polymerase I |
| RA | NZ_CP022686 | 2,868,740 | T→G | 21.9% | Q22P (CAG→CCG) | fdoH ← | formate dehydrogenase O subunit beta |
| RA | NZ_CP022686 | 2,950,876 | C→G | 60.5% | H26Q (CAC→CAG) | oxyR → | DNA‑binding transcriptional regulator OxyR |
| RA | NZ_CP022686 | 3,020,229 | T→G | 15.0% | V133G (GTC→GGC) | yjbB → | Na/Pi cotransporter family protein |
| 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 | 23.7% | 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 | 3,444,704 | T→G | 17.4% | T530P (ACC→CCC) | btsT ← | pyruvate/proton symporter BtsT |
| RA | NZ_CP022686 | 3,451,834 | C→A | 11.8% | H275N (CAT→AAT) | lgoD → | L‑galactonate oxidoreductase |
| RA | NZ_CP022686 | 3,461,229 | T→G | 30.8% | noncoding (84/87 nt) | CIW80_RS17340 ← | tRNA‑Leu |
| RA | NZ_CP022686 | 3,520,304 | A→C | 5.9% | N355T (AAC→ACC) | ileS → | isoleucine‑‑tRNA ligase |
| RA | NZ_CP022686 | 3,652,079 | T→G | 13.0% | 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 | 3,734,367 | T→G | 13.5% | F225V (TTT→GTT) | yafD → | endonuclease/exonuclease/phosphatase family protein |
| RA | NZ_CP022686 | 3,792,805 | A→G | 100% | Y421C (TAC→TGC) | fucP → | L‑fucose:H+ symporter permease |
| RA | NZ_CP022686 | 3,797,481 | T→G | 18.3% | L130V (TTA→GTA) ‡ | CIW80_RS19065 → | LacI family DNA‑binding transcriptional regulator |
| RA | NZ_CP022686 | 3,797,483 | A→T | 19.2% | L130F (TTA→TTT) ‡ | CIW80_RS19065 → | LacI family DNA‑binding transcriptional regulator |
| RA | NZ_CP022686 | 3,928,369 | T→G | 13.5% | W285G (TGG→GGG) | prpE → | propionate‑‑CoA ligase |
| RA | NZ_CP022686 | 3,935,324 | T→G | 18.3% | N705T (AAC→ACC) | lacZ ← | beta‑galactosidase |
| RA | NZ_CP022686 | 3,949,969 | T→G | 11.1% | D141A (GAC→GCC) | hemB ← | porphobilinogen synthase |
| RA | NZ_CP022686 | 4,118,534 | A→T | 8.5% | Y256N (TAC→AAC) | nfrA ← | bacteriophage adsorption protein NfrA |
| RA | NZ_CP022686 | 4,440,334 | A→G | 18.9% | Q797Q (CAA→CAG) | ftsK → | DNA translocase FtsK |
| RA | NZ_CP022686 | 4,632,182 | T→G | 10.2% | R276R (CGT→CGG) | mchF → | microcin export transporter peptidase/ATP‑binding subunit MchF |
| RA | NZ_CP022686 | 4,642,938 | A→C | 9.9% | T728P (ACG→CCG) | sfaF → | S/F1C fimbrial usher SfaF/FocD |
| 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 | 4,951,531 | C→A | 11.6% | S42* (TCA→TAA) | topA → | type I DNA topoisomerase |
| RA | NZ_CP022686 | 5,041,191 | G→A | 8.2% | A274A (GCG→GCA) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,041,356 | T→A | 9.4% | G329G (GGT→GGA) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,043,300 | C→T | 7.2% | G977G (GGC→GGT) | 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] | |
| RA | pMut‑Ompa‑D5‑IL2wt‑His6 | 3,637 | C→G | 94.3% | T10S (ACC→AGC) ‡ | IL2wt no signal → | |
| RA | pMut‑Ompa‑D5‑IL2wt‑His6 | 3,638 | C→G | 94.6% | T10T (ACC→ACG) ‡ | IL2wt no signal → | |
| RA | pMut‑Ompa‑D5‑IL2wt‑His6 | 3,639 | C→T | 94.5% | Q11* (CAG→TAG) | IL2wt no signal → | |
| RA | pMut‑Ompa‑D5‑IL2wt‑His6 | 3,642 | C→G | 94.4% | L12V (CTG→GTG) ‡ | IL2wt no signal → | |
| RA | pMut‑Ompa‑D5‑IL2wt‑His6 | 3,643 | T→G | 94.5% | L12R (CTG→CGG) ‡ | IL2wt no signal → | |
| RA | pMut‑Ompa‑D5‑IL2wt‑His6 | 4,841 | G→T | 14.2% | intergenic (‑206/+368) | annotated as hok_sok locus ← / ← putative HTH domain protein | –/– |
| RA | pMut‑Ompa‑D5‑IL2wt‑His6 | 4,868 | Δ1 bp | 100% | intergenic (‑233/+341) | annotated as hok_sok locus ← / ← putative HTH domain protein | –/– |
| RA | pMut‑Ompa‑D5‑IL2wt‑His6 | 4,913 | A→T | 8.2% | intergenic (‑278/+296) | annotated as hok_sok locus ← / ← putative HTH domain protein | –/– |
| RA | pMut‑Ompa‑D5‑IL2wt‑His6 | 4,915 | G→T | 9.6% | intergenic (‑280/+294) | annotated as hok_sok locus ← / ← putative HTH domain protein | –/– |
| RA | pMut‑Ompa‑D5‑IL2wt‑His6 | 4,916 | G→T | 10.1% | intergenic (‑281/+293) | annotated as hok_sok locus ← / ← putative HTH domain protein | –/– |
| RA | pMut‑Ompa‑D5‑IL2wt‑His6 | 4,922 | G→T | 13.7% | intergenic (‑287/+287) | annotated as hok_sok locus ← / ← putative HTH domain protein | –/– |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NZ_MW240712 | 189–2618 | 3086–2957 | 340–2898 | 11253 [10377] | [11078] 11569 | JNG15_RS00005–mobA | JNG15_RS00005,JNG15_RS00010,JNG15_RS00015,mobA |