mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.1 revision aa8f2595a244
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 254,408 | A→G | F437L (TTC→CTC) | pepD ← | aminoacyl‑histidine dipeptidase (peptidase D) |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 371,588 | (G)6→7 | coding (350/867 nt) | mhpC → | 2‑hydroxy‑6‑ketonona‑2,4‑dienedioic acid hydrolase |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | regulator protein that represses frmRAB operon/outer membrane protein |
| RA | 505,757 | G→A | G282S (GGC→AGC) | ushA → | bifunctional UDP‑sugar hydrolase/5'‑nucleotidase |
| RA | 536,135 | T→C | I142I (ATT→ATC) | hyi → | hydroxypyruvate isomerase |
| RA | 573,440 | C→T | R24C (CGC→TGC) | rusA → | DLP12 prophage, endonuclease RUS |
| RA | 585,217 | C→T | W139* (TGG→TGA) | ompT ← | DLP12 prophage, outer membrane protease VII, outer membrane protein 3b |
| RA | 631,934 | A→G | T681A (ACG→GCG) | cstA → | carbon starvation protein involved in peptide utilization, APC peptide transporter family protein |
| RA | 792,525 | A→G | L422L (TTG→CTG) | modF ← | molybdate ABC transporter ATPase |
| RA | 806,505 | G→A | S259S (AGC→AGT) | ybhC ← | acyl‑CoA thioesterase, lipoprotein |
| RA | 852,261 | A→G | Y113H (TAC→CAC) | opgE ← | OPG biosynthetic transmembrane phosphoethanolamine transferase |
| RA | 902,473 | G→A | F172F (TTC→TTT) | artI ← | arginine transporter subunit |
| RA | 1,030,407 | A→G | F88L (TTT→CTT) | tusE ← | mnm(5)‑s(2)U34‑tRNA 2‑thiolation sulfurtransferase |
| RA | 1,037,227 | C→T | P160L (CCC→CTC) | hyaF → | hydrogenase‑1 protein nickel incorporation factor |
| RA | 1,043,741 | A→G | V157A (GTT→GCT) | etk ← | tyrosine‑protein kinase, role in O‑antigen capsule formation |
| RA | 1,044,364 | T→C | T105A (ACA→GCA) | etp ← | O‑antigen capsule forming protein‑tyrosine‑phosphatase, Etk‑P dephosphorylase |
| RA | 1,136,783 | T→C | V170V (GTT→GTC) | flgI → | putative flagellar basal body protein |
| RA | 1,249,389 | G→A | A123A (GCC→GCT) | dhaL ← | dihydroxyacetone kinase, C‑terminal domain |
| RA | 1,276,719 | A→G | F300F (TTT→TTC) | narX ← | sensory histidine kinase in two‑component regulatory system with NarL |
| RA | 1,285,372 | A→G | E78E (GAA→GAG) | narJ → | molybdenum‑cofactor‑assembly chaperone delta subunit of nitrate reductase 1 |
| RA | 1,287,826 | C→T | A267T (GCA→ACA) | purU ← | formyltetrahydrofolate hydrolase |
| RA | 1,318,967 | G→A | D274D (GAC→GAT) | trpC ← | indole‑3‑glycerolphosphate synthetase and N‑(5‑phosphoribosyl)anthranilate isomerase |
| RA | 1,416,279 | A→G | S370P (TCC→CCC) | recE ← | Rac prophage, exonuclease VIII, 5' to 3' specific dsDNA exonuclease |
| RA | 1,419,721 | (G)7→8 | intergenic (‑265/+44) | ydaG ← / ← racR | Rac prophage, uncharacterized protein/Rac prophage, putative DNA‑binding transcriptional regulator |
| RA | 1,458,573 | T→C | C104R (TGT→CGT) | paaG → | 1,2‑epoxyphenylacetyl‑CoA isomerase, oxepin‑CoA‑forming |
| RA | 1,458,617 | A→G | A118A (GCA→GCG) | paaG → | 1,2‑epoxyphenylacetyl‑CoA isomerase, oxepin‑CoA‑forming |
| RA | 1,595,427 | A→G | pseudogene (2561/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,610,596 | C→T | A29T (GCC→ACC) | uxaB ← | altronate oxidoreductase, NAD‑dependent |
| RA | 1,677,937 | T→C | intergenic (‑34/‑490) | pntA ← / → ydgH | pyridine nucleotide transhydrogenase, alpha subunit/DUF1471 family periplasmic protein |
| RA | 1,738,343 | A→G | Y167C (TAC→TGC) | purR → | transcriptional repressor, hypoxanthine‑binding |
| RA | 1,818,420 | A→G | R27R (CGT→CGC) | chbF ← | phospho‑chitobiase, general 6‑phospho‑beta‑glucosidase activity |
| RA | 1,893,102 | G→A | A45V (GCA→GTA) | yoaA ← | putative ATP‑dependent helicase, DinG family |
| RA | 1,904,586 | T→C | V231A (GTC→GCC) | manZ → | mannose‑specific enzyme IID component of PTS |
| RA | 1,907,539 | T→C | Y18C (TAC→TGC) | yobF ← | DUF2527 family heat‑induced protein |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,013,640 | T→C | S138P (TCT→CCT) | fliF → | flagellar basal‑body MS‑ring and collar protein |
| RA | 2,073,151 | T→C | L538P (CTG→CCG) | flu → | CP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| RA | 2,127,360 | T→C | T319A (ACG→GCG) | gmd ← | GDP‑D‑mannose dehydratase, NAD(P)‑binding |
| 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 | 2,198,006 | T→G | pseudogene (1533/2847 nt) | yehH → | DUF4132 family pseudogene, defective yehI paralog, molybdate metabolism regulator, first fragment, molybdate metabolism regulator, second fragment 2, yehI' molR mutations have phenotypes and the N‑terminal molR fragment of yehI' may be expressed and may have retained or evolved MolR function |
| RA | 2,248,780 | C→T | R280Q (CGG→CAG) | yeiE ← | putative DNA‑binding transcriptional regulator |
| RA | 2,258,486 | G→A | P271S (CCG→TCG) | psuK ← | pseudouridine kinase |
| RA | 2,288,554 | G→C | pseudogene (361/2525 nt) | yejO ← | pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system |
| RA | 2,346,057 | T→C | L398P (CTG→CCG) | nrdA → | ribonucleoside‑diphosphate reductase 1, alpha subunit |
| RA | 2,393,110 | T→C | intergenic (‑69/+95) | nuoM ← / ← nuoL | NADH:ubiquinone oxidoreductase, membrane subunit M/NADH:ubiquinone oxidoreductase, membrane subunit L |
| RA | 2,401,103 | G→A | T151T (ACC→ACT) | nuoF ← | NADH:ubiquinone oxidoreductase, chain F |
| RA | 2,426,492 | A→G | R99R (CGT→CGC) | hisJ ← | histidine ABC transporter periplasmic binding protein |
| RA | 2,474,356 | G→A | A109T (GCC→ACC) | yfdQ → | CPS‑53 (KpLE1) prophage, uncharacterized protein |
| RA | 2,763,869 | (T)7→8 | coding (1285/1617 nt) | yfjL ← | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein |
| RA | 2,767,500 | T→C | intergenic (+145/‑210) | rnlB → / → yfjP | CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, 50S ribosome‑binding GTPase family protein |
| RA | 2,842,591 | T→C | L151L (TTA→TTG) | hycI ← | protease involved in processing C‑terminal end of HycE |
| RA | 2,867,926 | (C)6→7 | coding (828/1140 nt) | nlpD ← | activator of AmiC murein hydrolase activity, lipoprotein |
| RA | 2,910,133 | C→T | V185I (GTC→ATC) | mazG ← | nucleoside triphosphate pyrophosphohydrolase |
| RA | 2,937,802 | A→G | D112G (GAC→GGC) | fucK → | L‑fuculokinase |
| RA | 3,043,412 | G→A | A71V (GCA→GTA) | yqfB ← | UPF0267 family protein |
| RA | 3,139,583 | G→A | R286H (CGT→CAT) | yghU → | putative S‑transferase |
| RA | 3,222,930 | G→A | D100N (GAT→AAT) | ebgA → | evolved beta‑D‑galactosidase, alpha subunit |
| RA | 3,263,580 | A→G | C27C (TGT→TGC) | tdcD ← | propionate kinase/acetate kinase C, anaerobic |
| RA | 3,271,600 | (C)5→6 | coding (171/1146 nt) | garK ← | glycerate kinase I |
| RA | 3,280,946 | G→A | pseudogene (246/375 nt) | agaW → | pseudogene, N‑acetylgalactosamine‑specific enzyme IIC component of PTS,enzyme, Central intermediary metabolism: Amino sugars, PTS system N‑acetylgalactosameine‑specific IIC component 2 |
| RA | 3,366,953 | G→A | G10R (GGA→AGA) | yhcF → | putative transcriptional regulator |
| RA | 3,379,266 | (C)7→8 | coding (732/1128 nt) | zapE ← | divisome ATPase |
| RA | 3,386,276 | A→G | V638A (GTA→GCA) | aaeB ← | p‑hydroxybenzoic acid efflux system component |
| RA | 3,388,394 | T→C | M245V (ATG→GTG) | aaeA ← | p‑hydroxybenzoic acid efflux system component |
| RA | 3,440,113 | A→G | V306A (GTG→GCG) | rpoA ← | RNA polymerase, alpha subunit |
| RA | 3,450,125 | T→C | T37A (ACC→GCC) | rplV ← | 50S ribosomal subunit protein L22 |
| RA | 3,457,094 | A→G | I240V (ATC→GTC) | gspD → | general secretory pathway component, cryptic |
| RA | 3,469,498 | T→C | Q119R (CAG→CGG) | chiA ← | periplasmic endochitinase |
| RA | 3,541,927 | T→C | R507R (CGT→CGC) | feoB → | ferrous iron transporter protein B and GTP‑binding protein, membrane protein |
| RA | 3,551,631 | T→C | V281V (GTA→GTG) | malP ← | maltodextrin phosphorylase |
| 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 |
| MC JC | 3,653,231 | Δ2,028 bp | IS5‑mediated | [yhiS]–[yhiD] | [yhiS], slp, dctR, [yhiD] |
| RA | 3,791,004 | A→G | G114G (GGT→GGC) | tdh ← | L‑threonine 3‑dehydrogenase, NAD(P)‑binding |
| RA | 3,815,808 | (A)8→7 | intergenic (‑40/+26) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH |
| RA | 3,831,457 | (G)5→4 | coding (1001/1710 nt) | yicH → | putative inner membrane‑anchored periplasmic AsmA family protein |
| RA | 3,901,765 | G→A | G152G (GGC→GGT) | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,928,356 | C→T | A416A (GCG→GCA) | viaA ← | stimulator of RavA ATPase activity, von Willebrand factor domain protein |
| RA | 3,936,381 | C→T | T35M (ACG→ATG) | rbsB → | D‑ribose ABC transporter periplasmic binding protein, ribose chemotaxis receptor |
| RA | 4,185,540 | C→T | P64L (CCG→CTG) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,199,332 | C→T | S181S (AGC→AGT) | nfi → | endonuclease V, deoxyinosine 3' endonuclease |
| RA | 4,225,294 | A→G | G489G (GGA→GGG) | metH → | homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent |
| RA | 4,229,765 | A→G | A126A (GCT→GCC) | pepE ← | peptidase E, alpha‑aspartyl dipeptidase |
| RA | 4,242,259 | A→G | intergenic (‑5/+367) | xylE ← / ← malG | D‑xylose transporter/maltose transporter subunit |
| RA | 4,281,472 | A→G | E498G (GAG→GGG) | yjcE → | putative cation/proton antiporter |
| RA | 4,285,518 | A→G | I618I (ATT→ATC) | acs ← | acetyl‑CoA synthetase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,341,750 | G→A | intergenic (‑122/‑161) | melR ← / → melA | melibiose operon transcriptional regulator, autoregulator/alpha‑galactosidase, NAD(P)‑binding |
| RA | 4,351,093 | G→A | G190G (GGC→GGT) | dcuS ← | sensory histidine kinase in two‑component regulatory system with DcuR, regulator of anaerobic fumarate respiration |
| RA | 4,490,935 | A→G | L69L (TTG→CTG) | idnR ← | transcriptional repressor, 5‑gluconate‑binding |
| RA | 4,538,491 | C→T | G92D (GGC→GAC) | nanM ← | N‑acetylneuraminic acid mutarotase |
| RA | 4,544,910 | G→A | V203M (GTG→ATG) | fimC → | periplasmic chaperone |
| RA | 4,574,101 | T→C | pseudogene (183/2937 nt) | yjiV → | pseudogene, conserved hypothetical protein |
| RA | 4,574,259 | A→G | pseudogene (341/2937 nt) | yjiV → | pseudogene, conserved hypothetical protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 807331 | 810370 | 3040 | 16 [14] | [14] 18 | ybhB–[bioB] | ybhB, bioA, [bioB] |
| * | * | ÷ | NC_000913 | 2857129 | 2859618 | 2490 | 19 [14] | [12] 15 | mutS | methyl‑directed mismatch repair protein |
| * | * | ÷ | NC_000913 | 3423716–3424230 | 3424544–3424243 | 14–829 | 18 [14] | [14] 17 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 46 (0.740) | 22 (0.410) | 20/182 | 1.3 | 32.3% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 53 (1.000) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 46 (0.740) | 13 (0.240) | 11/182 | 2.7 | 22.0% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 53 (1.000) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 47 (0.780) | 32/206 | 0.6 | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||