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 | 40,676 | G→A | T419I (ACC→ATC) | caiT ← | putative transporter |
| RA | 113,831 | G→A | V130M (GTG→ATG) | guaC → | GMP reductase |
| RA | 164,205 | A→G | S701G (AGT→GGT) | hrpB → | putative ATP‑dependent helicase |
| RA | 201,558 | A→G | P196P (CCA→CCG) | lpxD → | UDP‑3‑O‑(3‑hydroxymyristoyl)‑glucosamine N‑acyltransferase |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 293,780 | (A)7→6 | coding (139/699 nt) | yagL ← | CP4‑6 prophage, DNA‑binding protein |
| RA | 322,098 | C→T | T164I (ACC→ATC) | ykgE → | cysteine‑rich LutA family protein, putative electron transport chain YkgEFG component |
| RA | 337,217 | T→C | V147A (GTC→GCC) | yahF → | putative NAD(P)‑binding succinyl‑CoA synthase |
| RA | 573,440 | C→T | R24C (CGC→TGC) | rusA → | DLP12 prophage, endonuclease RUS |
| MC JC | 575,786 | Δ31,596 bp | IS5‑mediated | [nmpC]–[ybdK] | 34 genes [nmpC], essD, rrrD, rzpD, rzoD, borD, ybcV, ybcW, ylcI, nohD, aaaD, tfaD, ybcY, ybcY, tfaX, appY, ompT, pauD, envY, ybcH, nfrA, nfrB, cusS, cusR, cusC, cusF, cusB, cusA, pheP, ybdG, nfsB, ybdF, ybdJ, [ybdK] |
| RA | 683,121 | C→T | A91A (GCG→GCA) | hscC ← | Hsp70 family chaperone Hsc62, RpoD‑binding transcription inhibitor |
| RA | 742,336 | C→T | G74D (GGC→GAC) | dtpD ← | dipeptide and tripeptide permease D |
| RA | 895,545 | T→C | R185R (CGT→CGC) | potG → | putrescine ABC transporter ATPase |
| RA | 924,093 | A→G | D277G (GAC→GGC) | clpA → | ATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity |
| RA | 1,121,934 | A→G | I225T (ATC→ACC) | pyrC ← | dihydro‑orotase |
| RA | 1,201,128 | T→C | intergenic (‑96/‑369) | xisE ← / → ymfI | e14 prophage, putative excisionase/e14 prophage, uncharacterized protein |
| RA | 1,287,826 | C→T | A267T (GCA→ACA) | purU ← | formyltetrahydrofolate hydrolase |
| JC JC | 1,293,196 | IS5 (+) +4 bp | intergenic (‑274/‑328) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| 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 | 1,351,196 | (G)7→8 | intergenic (‑157/+211) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/DUF559 family endonuclease‑related protein |
| RA | 1,361,052 | (A)6→7 | intergenic (‑144/‑68) | puuA ← / → puuD | glutamate‑‑putrescine ligase/gamma‑glutamyl‑gamma‑aminobutyrate hydrolase |
| RA | 1,399,985 | (C)7→8 | coding (252/516 nt) | ogt ← | O‑6‑alkylguanine‑DNA:cysteine‑protein methyltransferase |
| RA | 1,407,462 | T→C | T112A (ACG→GCG) | ydaM ← | diguanylate cyclase, csgD regulator |
| RA | 1,432,289 | G→A | G1081S (GGT→AGT) | stfR → | Rac prophage, putative tail fiber protein |
| 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 | 1,846,908 | A→G | V18A (GTC→GCC) | topB ← | DNA topoisomerase III |
| RA | 1,904,586 | T→C | V231A (GTC→GCC) | manZ → | mannose‑specific enzyme IID component of PTS |
| RA | 1,927,241 | (C)6→7 | coding (1599/2061 nt) | ptrB ← | protease II |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,073,094 | T→C | L519P (CTG→CCG) | flu → | CP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| RA | 2,135,962 | T→A | D46V (GAT→GTT) | wzb ← | colanic acid production protein‑tyrosine‑phosphatase, Wzc‑P dephosphorylase |
| RA | 2,141,143 | A→G | L157P (CTG→CCG) | asmA ← | suppressor of OmpF assembly mutants, putative outer membrane protein assembly factor, inner membrane‑anchored periplasmic protein |
| RA | 2,143,783 | T→C | L173P (CTG→CCG) | 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 | 2,215,997 | A→G | R160R (CGT→CGC) | yehW ← | putative ABC transporter permease |
| RA | 2,248,780 | C→T | R280Q (CGG→CAG) | yeiE ← | putative DNA‑binding transcriptional regulator |
| RA | 2,253,271 | G→A | A292V (GCC→GTC) | nupX ← | nucleoside permease |
| RA | 2,284,097 | T→C | intergenic (‑150/‑32) | yejK ← / → yejL | spermidine nucleoid‑associated protein/UPF0352 family protein |
| RA | 2,313,434 | T→C | intergenic (+258/‑54) | micF → / → rcsD | sRNA antisense regulator affecting ompF expression, Hfq‑dependent/phosphotransfer intermediate protein in two‑component regulatory system with RcsBC |
| RA | 2,401,103 | G→A | T151T (ACC→ACT) | nuoF ← | NADH:ubiquinone oxidoreductase, chain F |
| RA | 2,512,258 | (T)5→6 | coding (449/1239 nt) | mntH ← | manganese/divalent cation transporter |
| RA | 2,672,123 | G→A | G26E (GGG→GAG) | hcaD → | phenylpropionate dioxygenase, ferredoxin reductase subunit |
| RA | 2,704,009 | G→A | H19Y (CAT→TAT) | rnc ← | RNase III |
| RA | 2,734,543 | (C)8→9 | coding (492/732 nt) | yfiH ← | UPF0124 family 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 | 2,842,591 | T→C | L151L (TTA→TTG) | hycI ← | protease involved in processing C‑terminal end of HycE |
| RA | 2,863,165 | T→C | R277R (CGT→CGC) | ygbK → | FliA‑regulated DUF1537 family protein |
| RA | 2,895,747 | C→T | E11E (GAG→GAA) | ygcQ ← | putative flavoprotein |
| RA | 2,937,802 | A→G | D112G (GAC→GGC) | fucK → | L‑fuculokinase |
| RA | 3,139,583 | G→A | R286H (CGT→CAT) | yghU → | putative S‑transferase |
| RA | 3,218,665 | T→C | T138A (ACC→GCC) | aer ← | fused signal transducer for aerotaxis sensory component/methyl accepting chemotaxis component |
| RA | 3,271,600 | (C)5→6 | coding (171/1146 nt) | garK ← | glycerate kinase I |
| RA | 3,342,683 | T→C | G137G (GGT→GGC) | kdsC → | 3‑deoxy‑D‑manno‑octulosonate 8‑phosphate phosphatase |
| RA | 3,366,953 | G→A | G10R (GGA→AGA) | yhcF → | putative transcriptional regulator |
| RA | 3,428,954 | G→A | intergenic (‑192/‑282) | rrsD ← / → yrdA | 16S ribosomal RNA of rrnD operon/bacterial transferase hexapeptide domain protein |
| RA | 3,451,938 | G→A | R117C (CGT→TGT) | rplD ← | 50S ribosomal subunit protein L4 |
| RA | 3,457,094 | A→G | I240V (ATC→GTC) | gspD → | general secretory pathway component, cryptic |
| 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 | 3,648,024 | T→C | intergenic (‑236/‑39) | dinQ ← / → agrA | UV‑inducible membrane toxin, DinQ‑AgrB type I toxin‑antitoxin system/inactive antisense sRNA |
| RA | 3,791,004 | A→G | G114G (GGT→GGC) | tdh ← | L‑threonine 3‑dehydrogenase, NAD(P)‑binding |
| RA | 3,798,803 | T→C | T170T (ACA→ACG) | waaU ← | lipopolysaccharide core biosynthesis |
| RA | 3,815,811 | C→T | intergenic (‑43/+23) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH |
| RA | 3,830,989 | T→C | V178A (GTT→GCT) | yicH → | putative inner membrane‑anchored periplasmic AsmA family protein |
| RA | 3,894,654 | G→A | M1M (ATG→ATA) † | chrR → | chromate reductase, Class I, flavoprotein |
| RA | 3,901,765 | G→A | G152G (GGC→GGT) | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,936,381 | C→T | T35M (ACG→ATG) | rbsB → | D‑ribose ABC transporter periplasmic binding protein, ribose chemotaxis receptor |
| RA | 4,079,101 | A→G | intergenic (+663/‑196) | yiiD → / → yiiE | GNAT family putative N‑acetyltransferase/CopG family putative transcriptional regulator |
| RA | 4,187,838 | A→G | D830G (GAC→GGC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,281,472 | A→G | E498G (GAG→GGG) | yjcE → | putative cation/proton antiporter |
| RA | 4,291,336 | C→T | G287G (GGC→GGT) | nrfD → | formate‑dependent nitrite reductase, membrane subunit |
| RA | 4,293,898 | A→G | Y119C (TAC→TGC) | nrfG → | heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfG |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| 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 | 4,574,259 | A→G | pseudogene (341/2937 nt) | yjiV → | pseudogene, conserved hypothetical protein |
| RA | 4,606,094 | (G)8→7 | noncoding (72/87 nt) | leuV ← | tRNA‑Leu |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 807337 | 810365 | 3029 | 10 [9] | [9] 10 | ybhB–[bioB] | ybhB, bioA, [bioB] |
| * | * | ÷ | NC_000913 | 1465157 | 1465234 | 78 | 13 [9] | [9] 10 | ynbG | ynbG |
| * | * | ÷ | NC_000913 | 2857138 | 2859614 | 2477 | 15 [0] | [9] 15 | mutS | methyl‑directed mismatch repair protein |
| * | * | ÷ | NC_000913 | 3423759–3424234 | 3424530–3424239 | 6–772 | 10 [9] | [9] 10 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| * | * | ÷ | NC_000913 | 3944158–3945566 | 3945788–3945569 | 4–1631 | 10 [9] | [8] 10 | rrlC | 23S ribosomal RNA of rrnC operon |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 46 (0.890) | 13 (0.290) | 11/194 | 2.0 | 26.7% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 32 (0.720) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||