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 | 12,125 | A→C | intergenic (‑339/‑38) | yaaI ← / → dnaK | DUF2541 family protein/molecular chaperone DnaK |
RA | 44,049 | A→G | I288V (ATC→GTC) | fixB → | electron transfer flavoprotein subunit alpha/FixB family protein |
RA | 100,843 | T→C | H125H (CAT→CAC) | ftsA → | cell division protein FtsA |
RA | 136,175 | T→C | E513G (GAA→GGA) | gcd ← | quinoprotein glucose dehydrogenase |
RA | 232,843 | T→C | I97T (ATC→ACC) | dnaQ → | DNA polymerase III subunit epsilon |
RA | 245,728 | A→G | pseudogene (830/1713 nt) | BW25113_RS01160 ← | flagellar biosynthesis protein FlhA |
RA | 258,435 | A→G | I408V (ATC→GTC) | proA → | glutamate‑5‑semialdehyde dehydrogenase |
RA | 392,218 | T→C | S42P (TCC→CCC) | sbmA → | peptide antibiotic transporter SbmA |
RA | 427,262 | A→C | F70V (TTC→GTC) | tsx ← | nucleoside‑specific channel‑forming protein Tsx |
RA | 444,604 | T→C | A498A (GCA→GCG) | cyoB ← | cytochrome o ubiquinol oxidase subunit I |
RA | 450,563 | G→A | intergenic (+318/‑26) | bolA → / → tig | transcriptional regulator BolA/trigger factor |
RA | 454,444 | A→G | E34G (GAA→GGA) | lon → | endopeptidase La |
RA | 500,156 | A→G | intergenic (‑4/‑214) | fsr ← / → ushA | fosmidomycin MFS transporter/bifunctional UDP‑sugar hydrolase/5'‑nucleotidase |
RA | 538,997 | T→C | D169G (GAT→GGT) | allE ← | (S)‑ureidoglycine aminohydrolase |
RA | 656,002 | T→C | E278G (GAA→GGA) | ybeF ← | YbeF family transcriptional regulator |
RA | 710,687 | T→C | intergenic (+33/‑181) | pgm → / → BW25113_RS03560 | phosphoglucomutase (alpha‑D‑glucose‑1,6‑bisphosphate‑dependent)/lipoprotein |
RA | 797,607 | A→C | T89P (ACC→CCC) | ybhI → | anion permease |
RA | 838,798 | A→G | V713V (GTT→GTC) | ybiO ← | mechanosensitive channel protein |
RA | 847,509 | T→C | D182G (GAT→GGT) | opgE ← | phosphoethanolamine transferase |
RA | 933,331 | T→C | D168D (GAT→GAC) | lolA → | outer membrane lipoprotein chaperone LolA |
RA | 989,508 | C→G | A261P (GCC→CCC) | ssuC ← | aliphatic sulfonate ABC transporter permease SsuC |
RA | 1,015,359 | T→C | T51A (ACC→GCC) | ompA ← | porin OmpA |
RA | 1,056,010 | T→C | I433I (ATT→ATC) | torA → | trimethylamine‑N‑oxide reductase TorA |
RA | 1,067,094 | A→G | V43A (GTC→GCC) | rutD ← | pyrimidine utilization protein D |
RA | 1,077,067 | T→C | pseudogene (256/830 nt) | BW25113_RS05295 → | FTR1 family protein |
RA | 1,084,094 | T→C | D407G (GAT→GGT) | pgaB ← | poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine N‑deacetylase PgaB |
RA | 1,185,332 | T→A | D191V (GAT→GTT) | phoP ← | two‑component system response regulator PhoP |
RA | 1,201,334 | T→C | pseudogene (148/408 nt) | BW25113_RS05975 → | phage portal protein |
RA | 1,343,839 | T→C | T176A (ACA→GCA) | yciW ← | CMD domain‑containing protein |
RA | 1,364,361 | T→C | intergenic (+101/‑112) | pspE → / → ycjM | thiosulfate sulfurtransferase PspE/glucosylglycerate phosphorylase |
RA | 1,393,322 | A→T | D154E (GAT→GAA) | fnr ← | fumarate/nitrate reduction transcriptional regulator Fnr |
RA | 1,443,321 | (T)7→6 | intergenic (+46/+12) | feaB → / ← tynA | phenylacetaldehyde dehydrogenase/primary‑amine oxidase |
RA | 1,473,944 | (G)6→7 | coding (550/1758 nt) | ynbC → | bifunctional alpha/beta hydrolase/class I SAM‑dependent methyltransferase |
RA | 1,494,141 | A→G | F189S (TTT→TCT) | ydcK ← | YdcK family protein |
RA | 1,749,862 | A→C | H37P (CAC→CCC) | BW25113_RS26160 → | protein YnhH |
RA | 1,759,822 | A→G | F23S (TTC→TCC) | menI ← | 1,4‑dihydroxy‑2‑naphthoyl‑CoA hydrolase |
RA | 1,764,071 | A→G | L247L (TTA→TTG) | ydiK → | AI‑2E family transporter YdiK |
RA | 1,841,981 | (C)6→5 | coding (285/1044 nt) | selD ← | selenide, water dikinase SelD |
RA | 1,907,320 | A→G | F585S (TTC→TCC) | prc ← | carboxy terminal‑processing peptidase |
RA | 1,943,712 | T→G | E356D (GAA→GAC) | aspS ← | aspartate‑‑tRNA ligase |
RA | 2,090,333 | A→G | D80G (GAC→GGC) | hisIE → | bifunctional phosphoribosyl‑AMP cyclohydrolase/phosphoribosyl‑ATP diphosphatase HisIE |
MC JC | 2,399,465 | Δ7 bp | coding (650‑656/939 nt) | lrhA ← | transcriptional regulator LrhA |
RA | 2,449,226 | A→G | intergenic (‑101/+580) | yfcV ← / ← sixA | fimbrial protein/phosphohistidine phosphatase SixA |
RA | 2,495,699 | A→G | S756P (TCC→CCC) | ptsP ← | phosphoenolpyruvate‑‑protein phosphotransferase |
RA | 2,545,923 | A→G | G71G (GGA→GGG) | amiA → | N‑acetylmuramoyl‑L‑alanine amidase AmiA |
RA | 2,549,285 | T→G | T159P (ACC→CCC) | eutL ← | ethanolamine utilization microcompartment protein EutL |
RA | 2,550,898 | T→C | I381V (ATC→GTC) | eutB ← | ethanolamine ammonia‑lyase subunit alpha |
RA | 2,769,064 | A→G | pseudogene (74/185 nt) | BW25113_RS24190 → | DUF905 domain‑containing protein |
RA | 2,929,425 | C→T | R161R (CGC→CGT) | fucI → | L‑fucose isomerase |
RA | 2,968,720 | T→C | G218G (GGA→GGG) | aas ← | bifunctional acyl‑ACP‑‑phospholipid O‑acyltransferase/long‑chain‑fatty‑acid‑‑ACP ligase |
RA | 2,972,615 | A→G | D79G (GAT→GGT) | lysR → | DNA‑binding transcriptional regulator LysR |
RA | 3,095,787 | A→G | F142S (TTC→TCC) | trmB ← | tRNA (guanosine(46)‑N7)‑methyltransferase TrmB |
RA | 3,255,828 | +G | coding (1192/1209 nt) | tdcD ← | propionate kinase |
RA | 3,427,745 | A→G | E58G (GAA→GGA) | fmt → | methionyl‑tRNA formyltransferase |
RA | 3,620,259 | A→T | D880E (GAT→GAA) | rbbA ← | ribosome‑associated ATPase/putative transporter RbbA |
RA | 3,736,824 | A→G | A244A (GCA→GCG) | yiaK → | 3‑dehydro‑L‑gulonate 2‑dehydrogenase |
RA | 3,758,726 | G→C | A1062P (GCC→CCC) | rhsA → | RHS element protein RhsA |
RA | 3,845,141 | A→G | I335T (ATC→ACC) | ilvB ← | acetolactate synthase large subunit |
RA | 3,935,432 | G→A | noncoding (265/1542 nt) | BW25113_RS19520 → | 16S ribosomal RNA |
RA | 4,004,376 | T→C | intergenic (+16/‑60) | yigL → / → bioP | sugar/pyridoxal phosphate phosphatase YigL/biotin transporter |
RA | 4,006,495 | C→G | A28G (GCG→GGG) | metE → | 5‑methyltetrahydropteroyltriglutamate‑‑ homocysteine S‑methyltransferase |
RA | 4,087,432 | A→G | intergenic (‑82/‑232) | rhaD ← / → rhaS | rhamnulose‑1‑phosphate aldolase/HTH‑type transcriptional activator RhaS |
RA | 4,258,591 | (T)6→5 | intergenic (+356/+146) | tyrB → / ← BW25113_RS26020 | aromatic amino acid transaminase/hypothetical protein |
Unassigned missing coverage evidence | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
seq id | start | end | size | ←reads | reads→ | gene | description | |||
* | * | ÷ | NZ_CP009273 | 356981 | 357567 | 587 | 4 [0] | [0] 3 | lacA | galactoside O‑acetyltransferase |
* | * | ÷ | NZ_CP009273 | 2505244 | 2505302 | 59 | 3 [2] | [2] 3 | mntH | Nramp family divalent metal transporter |
Unassigned new junction evidence | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | NZ_CP009273 | 360104 = | NA (NA) | 47 (1.330) | 26/164 | 0.2 | NA | intergenic (‑35/+251) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
? | NZ_CP009273 | = 360286 | NA (NA) | intergenic (‑217/+69) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein | |||||
* | ? | NZ_CP009273 | = 1391494 | NA (NA) | 23 (0.660) | 12/162 | 1.0 | 79.5% | intergenic (+145/‑128) | BW25113_RS06980/ynaJ | IS5‑like element IS5 family transposase/DUF2534 family protein |
? | NZ_CP009273 | 1972747 = | 6 (0.170) | intergenic (‑293/‑487) | flhD/uspC | flagellar transcriptional regulator FlhD/universal stress protein UspC | |||||
* | ? | NZ_CP009273 | = 1972751 | 0 (0.000) | 52 (1.470) | 33/164 | 0.1 | 100% | intergenic (‑297/‑483) | flhD/uspC | flagellar transcriptional regulator FlhD/universal stress protein UspC |
? | NZ_CP009273 | = 2283592 | NA (NA) | intergenic (‑68/‑387) | BW25113_RS11435/narP | IS5‑like element IS5 family transposase/nitrate/nitrite response regulator protein NarP | |||||
* | ? | NZ_CP009273 | = 4532507 | 20 (0.570) | 12 (0.380) | 7/146 | 1.5 | 34.4% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
? | NZ_CP009273 | = 4532803 | 28 (0.890) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |