mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.29.0 revision 8f9c342918e4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 134,458 | T→C | V24A (GTC→GCC) | yacL → | UPF0231 family protein |
| RA | 198,178 | T→C | L84P (CTT→CCT) | bamA → | BamABCDE complex OM biogenesis outer membrane pore‑forming assembly factor |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 277,597 | T→C | C295R (TGC→CGC) | mmuM → | CP4‑6 prophage; S‑methylmethionine:homocysteine methyltransferase |
| RA | 284,450 | A→G | E417G (GAG→GGG) | yagF → | CP4‑6 prophage; dehydratase family protein |
| RA | 309,778 | C→T | L83L (TTG→TTA) | ecpB ← | ECP production pilus chaperone |
| RA | 318,798 | T→C | M402V (ATG→GTG) | rclA ← | reactive chlorine stress species (RCS) resistance protein; pyridine nucleotide‑dependent disulfide oxidoreductase family |
| RA | 379,831 | A→G | R17R (CGT→CGC) | frmR ← | regulator protein that represses frmRAB operon |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | regulator protein that represses frmRAB operon/outer membrane protein |
| RA | 400,157 | T→C | Y256C (TAC→TGC) | ddlA ← | D‑alanine‑D‑alanine ligase A |
| RA | 451,552 | A→G | V20A (GTA→GCA) | cyoA ← | cytochrome o ubiquinol oxidase subunit II |
| RA | 460,036 | C→T | G383G (GGC→GGT) | lon → | DNA‑binding ATP‑dependent protease La |
| RA | 467,738 | T→C | G109G (GGT→GGC) | cof → | thiamine pyrimidine pyrophosphate hydrolase; HMP‑PP phosphatase |
| JC JC | 587,900 | IS2 (–) +5 bp | coding (78‑82/891 nt) | ybcH ← | PRK09936 family protein |
| RA | 599,828 | T→C | L372P (CTG→CCG) | cusA → | copper/silver efflux system, membrane component |
| RA | 602,007 | C→T | P17S (CCG→TCG) | pheP → | phenylalanine transporter |
| RA | 657,377 | T→C | V29A (GTG→GCG) | cspE → | constitutive cold shock family transcription antitermination protein; negative regulator of cspA transcription; RNA melting protein; ssDNA‑binding protein |
| RA | 657,830 | T→C | T37A (ACG→GCG) | flc ← | fluoride efflux channel, dual topology membrane protein |
| RA | 783,506 | C→T | A114V (GCG→GTG) | pnuC → | nicotinamide riboside transporter |
| RA | 871,451 | T→C | L162P (CTG→CCG) | gsiC → | glutathione ABC transporter permease |
| RA | 903,872 | (G)5→6 | intergenic (‑138/+80) | artP ← / ← ybjP | arginine ABC transporter ATPase/lipoprotein |
| RA | 909,056 | T→C | Q80R (CAG→CGG) | ltaE ← | L‑allo‑threonine aldolase, PLP‑dependent |
| RA | 977,322 | G→A | A333T (GCC→ACC) | mukB → | chromosome condensin MukBEF, ATPase and DNA‑binding subunit |
| RA | 1,043,741 | A→G | V157A (GTT→GCT) | etk ← | tyrosine‑protein kinase, role in O‑antigen capsule formation |
| RA | 1,076,582 | A→G | R767R (CGT→CGC) | putA ← | fused DNA‑binding transcriptional regulator/proline dehydrogenase/pyrroline‑5‑carboxylate dehydrogenase |
| RA | 1,084,191 | A→G | V272V (GTA→GTG) | efeB → | deferrrochelatase, periplasmic |
| RA | 1,089,445 | (G)5→4 | coding (413/2019 nt) | pgaB ← | poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine (PGA) N‑deacetylase outer membrane export lipoprotein |
| RA | 1,129,652 | C→T | R60H (CGC→CAC) | flgN ← | export chaperone for FlgK and FlgL |
| RA | 1,140,553 | A→G | H174R (CAC→CGC) | flgL → | flagellar hook‑filament junction protein |
| RA | 1,169,838 | T→C | G179G (GGA→GGG) | ldtC ← | L,D‑transpeptidase linking Lpp to murein |
| RA | 1,196,495 | T→C | intergenic (+122/+372) | icd → / ← ymfD | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase/e14 prophage; putative SAM‑dependent methyltransferase |
| RA | 1,216,705 | A→G | intergenic (+70/‑43) | ariR → / → ymgC | RcsB connector protein for regulation of biofilm and acid‑resistance/Blue light, low temperature and stress induced protein |
| RA | 1,297,386 | A→G | C246R (TGT→CGT) | adhE ← | fused acetaldehyde‑CoA dehydrogenase/iron‑dependent alcohol dehydrogenase/pyruvate‑formate lyase deactivase |
| MC JC | 1,299,499 | Δ1,199 bp | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,307,916 | C→T | D244N (GAT→AAT) | clsA ← | cardiolipin synthase 1 |
| RA | 1,312,802 | A→T | I30N (ATC→AAC) | yciB ← | IspA family inner membrane protein |
| RA | 1,323,187 | C→T | intergenic (‑105/‑33) | trpL ← / → yciV | trp operon leader peptide/PHP domain protein |
| RA | 1,390,211 | C→T | D130N (GAC→AAC) | mpaA ← | murein peptide amidase A |
| RA | 1,499,529 | A→G | G307G (GGT→GGC) | ydcK ← | uncharacterized protein |
| RA | 1,664,969 | T→C | L155P (CTT→CCT) | dmsD → | twin‑argninine leader‑binding protein for DmsA and TorA |
| RA | 1,756,617 | A→G | D307G (GAC→GGC) | pykF → | pyruvate kinase I |
| RA | 1,769,479 | A→G | T136A (ACG→GCG) | ydiK → | UPF0118 family inner membrane protein |
| RA | 1,793,850 | (C)6→7 | coding (260/552 nt) | btuE ← | glutathione peroxidase |
| JC JC | 1,825,955 | IS5 (–) +4 bp | coding (966‑969/969 nt) | astE ← | succinylglutamate desuccinylase |
| RA | 1,870,836 | T→C | L151P (CTG→CCG) | yeaI → | putative membrane‑anchored diguanylate cyclase |
| RA | 1,876,662 | G→A | A330A (GCG→GCA) | yeaN → | putative MFS transporter, inner membrane protein |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (+) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 family protein, nitrate‑inducible |
| RA | 1,954,322 | T→C | L294P (CTG→CCG) | cmoB → | tRNA (cmo5U34)‑carboxymethyltransferase, carboxy‑SAM‑dependent |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,065,589 | T→C | E59G (GAG→GGG) | cobU ← | cobinamide kinase and cobinamide phosphate guanylyltransferase |
| RA | 2,143,684 | (G)6→7 | coding (419/3318 nt) | yegE → | putative diguanylate cyclase |
| RA | 2,173,363 | Δ2 bp | intergenic (‑1/+1) | gatC ← / ← gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,214,702 | T→C | intergenic (‑58/‑164) | yehU ← / → mlrA | inner membrane putative sensory kinase in two‑component system with YehT/transcriptional activator of csgD and csgBA |
| RA | 2,222,366 | T→C | V61A (GTG→GCG) | dld → | D‑lactate dehydrogenase, FAD‑binding, NADH independent |
| RA | 2,317,917 | T→C | T654A (ACC→GCC) | rcsC ← | hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| RA | 2,419,171 | T→C | E2E (GAA→GAG) | yfcD ← | putative NUDIX hydrolase |
| RA | 2,485,315 | (C)6→7 | coding (942/3594 nt) | evgS → | hybrid sensory histidine kinase in two‑component regulatory system with EvgA |
| RA | 2,688,959 | A→G | V183A (GTT→GCT) | yfhG ← | putative outer membrane protein modulating the QseEF response |
| RA | 2,690,469 | A→G | R210R (CGT→CGC) | glrK ← | sensor protein kinase regulating glmY sRNA in two‑component system with response regulator GlrR |
| RA | 2,747,020 | G→A | A259V (GCG→GTG) | ffh ← | Signal Recognition Particle (SRP) component with 4.5S RNA (ffs) |
| JC | 2,765,463 | (TATGGCAC)6→7 | intergenic (‑310/+50) | yfjL ← / ← yfjM | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein/CP4‑57 prophage; uncharacterized protein |
| RA | 2,785,581 | T→C | intergenic (‑570/+181) | ypjC ← / ← ileY | pseudogene/tRNA‑Ile |
| RA | 2,809,534 | T→C | intergenic (+41/‑83) | ygaY → / → ygaZ | pseudogene, major facilitator transporter superfamily;putative transport; Not classified; putative transport protein/putative L‑valine exporter, norvaline resistance protein |
| RA | 2,858,929 | A→C | T613P (ACC→CCC) | mutS → | methyl‑directed mismatch repair protein |
| RA | 2,862,057 | T→C | Y210H (TAT→CAT) | ygbJ → | putative dehydrogenase |
| RA | 2,863,006 | T→C | G224G (GGT→GGC) | ygbK → | FliA‑regulated DUF1537 family protein |
| RA | 2,892,270 | A→G | P19P (CCA→CCG) | queD → | 6‑pyruvoyl tetrahydrobiopterin synthase (PTPS) |
| RA | 2,910,582 | T→C | Y35C (TAC→TGC) | mazG ← | nucleoside triphosphate pyrophosphohydrolase |
| RA | 2,913,035 | A→G | L206P (CTC→CCC) | relA ← | (p)ppGpp synthetase I/GTP pyrophosphokinase |
| RA | 2,913,196 | T→C | K152K (AAA→AAG) | relA ← | (p)ppGpp synthetase I/GTP pyrophosphokinase |
| RA | 2,957,284 | A→G | V534A (GTG→GCG) | ptrA ← | protease III |
| RA | 2,978,279 | A→G | A207A (GCT→GCC) | lysA ← | diaminopimelate decarboxylase, PLP‑binding |
| RA | 3,012,795 | T→C | N482S (AAC→AGC) | yqeB ← | XdhC‑CoxI family protein with NAD(P)‑binding Rossman fold |
| RA | 3,032,303 | (C)5→6 | coding (937/1449 nt) | uacT → | uric acid permease |
| RA | 3,122,268 | T→C | D513G (GAC→GGC) | glcB ← | malate synthase G |
| RA | 3,355,080 | T→C | V119A (GTC→GCC) | gltB → | glutamate synthase, large subunit |
| RA | 3,370,354 | A→G | V228A (GTG→GCG) | nanE ← | putative N‑acetylmannosamine‑6‑P epimerase |
| RA | 3,439,996 | G→A | R2C (CGC→TGC) | rplQ ← | 50S ribosomal subunit protein L17 |
| RA | 3,507,955 | G→A | G212G (GGC→GGT) | php ← | phosphotriesterase homology protein |
| RA | 3,560,455 | +G | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,590,692 | T→C | T74A (ACG→GCG) | ugpA ← | sn‑glycerol‑3‑phosphate ABC transporter permease |
| RA | 3,634,685 | G→A | intergenic (‑227/‑156) | yhiL ← / → yhiM | pseudogene, DUF4049 family protein/acid resistance protein, inner membrane |
| RA | 3,664,363 | (G)6→7 | coding (256/729 nt) | gadW ← | transcriptional activator of gadA and gadBC; repressor of gadX |
| RA | 3,684,183 | A→G | V479A (GTG→GCG) | yhjK ← | cyclic‑di‑GMP phosphodiesterase |
| RA | 3,723,735 | T→C | E221E (GAA→GAG) | glyS ← | glycine tRNA synthetase, beta subunit |
| RA | 3,815,808 | (A)8→7 | intergenic (‑40/+26) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| RA | 3,844,146 | T→C | G61G (GGT→GGC) | adeD → | cryptic adenine deaminase |
| RA | 3,940,705 | G→A | A208V (GCG→GTG) | yieP ← | putative transcriptional regulator |
| RA | 3,967,132 | A→G | H239R (CAC→CGC) | rho → | transcription termination factor |
| RA | 3,982,684 | (C)8→9 | noncoding (79/87 nt) | leuT → | tRNA‑Leu |
| RA | 3,988,580 | T→C | K163E (AAA→GAA) | hemX ← | putative uroporphyrinogen III methyltransferase |
| RA | 4,011,598 | T→C | W175R (TGG→CGG) | yigM → | putative inner membrane EamA‑like transporter |
| RA | 4,031,161 | (A)6→7 | coding (1/1332 nt) | pepQ → | proline dipeptidase |
| RA | 4,052,834 | C→T | Q264* (CAG→TAG) | hemN → | coproporphyrinogen III oxidase, SAM and NAD(P)H dependent, oxygen‑independent |
| RA | 4,128,197 | T→C | T67A (ACC→GCC) | metJ ← | transcriptional repressor, S‑adenosylmethionine‑binding |
| RA | 4,134,394 | A→G | D187G (GAC→GGC) | katG → | catalase‑peroxidase HPI, heme b‑containing |
| RA | 4,135,451 | A→G | K539K (AAA→AAG) | katG → | catalase‑peroxidase HPI, heme b‑containing |
| RA | 4,255,504 | G→A | H321H (CAC→CAT) | plsB ← | glycerol‑3‑phosphate O‑acyltransferase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,381,504 | T→C | E272G (GAA→GGA) | frdA ← | anaerobic fumarate reductase catalytic and NAD/flavoprotein subunit |
| RA | 4,382,351 | C→T | intergenic (‑33/‑292) | frdA ← / → epmA | anaerobic fumarate reductase catalytic and NAD/flavoprotein subunit/Elongation Factor P Lys34 lysyltransferase |
| RA | 4,410,053 | (T)9→8 | intergenic (+47/‑80) | rlmB → / → yjfI | 23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent/DUF2170 family protein |
| RA | 4,606,215 | (G)8→7 | noncoding (72/87 nt) | leuP ← | tRNA‑Leu |
| RA | 4,640,125 | T→C | N61S (AAC→AGC) | arcA ← | response regulator in two‑component regulatory system with ArcB or CpxA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423735–3424234 | 3424563–3424239 | 6–829 | 19 [18] | [18] 20 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 382276 | NA (NA) | 22 (0.510) | 21/294 | 1.9 | NA | noncoding (1017/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382590 | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 7 (0.160) | 28 (0.720) | 26/266 | 0.9 | 83.3% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 5 (0.130) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 7 (0.160) | 29 (0.740) | 28/266 | 0.7 | 83.8% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 5 (0.130) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1468228 | NA (NA) | 41 (0.940) | 37/298 | 0.4 | NA | noncoding (1013/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 1469240 | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||