mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | 95,633 | G→A | L328L (CTG→CTA) | murF → | UDP‑N‑acetylmuramoyl‑tripeptide:D‑alanyl‑D‑ alanine ligase |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 280,453 | T→C | pseudogene (283/309 nt) | yagB ← | pseudogene, CP4‑6 prophage,Phage or Prophage Related |
| RA | 323,702 | T→C | A455A (GCT→GCC) | ykgF → | ferridoxin‑like LutB family protein, putative electron transport chain YkgEFG component |
| RA | 509,678 | T→A | I568F (ATC→TTC) | copA ← | copper transporter |
| RA | 573,440 | C→T | R24C (CGC→TGC) | rusA → | DLP12 prophage, endonuclease RUS |
| JC JC | 585,480 | IS5 (+) +4 bp | coding (151‑154/954 nt) | ompT ← | DLP12 prophage, outer membrane protease VII, outer membrane protein 3b |
| RA | 640,165 | C→T | A138V (GCG→GTG) | ahpF → | alkyl hydroperoxide reductase, F52a subunit, FAD/NAD(P)‑binding |
| RA | 662,907 | G→A | Q353* (CAA→TAA) | dacA ← | D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 5) |
| RA | 773,987 | C→T | P316S (CCG→TCG) | cydB → | cytochrome d terminal oxidase, subunit II |
| RA | 1,287,826 | C→T | A267T (GCA→ACA) | purU ← | formyltetrahydrofolate hydrolase |
| RA | 1,423,484 | T→A | pseudogene (284/444 nt) C29S (TGC→AGC) |
rzpR → rzoR → |
pseudogene, Rac prophage, Bacteriophage Rz lysis protein family,Phage or Prophage Related, putative Rac prophage endopeptidase, completely contained in another CDS Rac prophage, putative lipoprotein |
| RA | 1,458,617 | A→G | A118A (GCA→GCG) | paaG → | 1,2‑epoxyphenylacetyl‑CoA isomerase, oxepin‑CoA‑forming |
| RA | 1,511,099 | G→A | R366H (CGC→CAC) | ydcR → | putative DNA‑binding transcriptional regulator and putative aminotransferase |
| RA | 1,595,427 | A→G | pseudogene (2561/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,685,542 | (C)6→7 | coding (1047/1404 nt) | fumC ← | fumarate hydratase (fumarase C),aerobic Class II |
| RA | 1,762,338 | T→C | T59A (ACG→GCG) | sufC ← | SufBCD Fe‑S cluster assembly scaffold protein, ATP‑binding protein |
| RA | 1,866,995 | C→T | Q30* (CAA→TAA) | yeaG → | protein kinase, endogenous substrate unidentified, autokinase |
| RA | 1,904,586 | T→C | V231A (GTC→GCC) | manZ → | mannose‑specific enzyme IID component of PTS |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 1,981,182 | C→T | R144Q (CGG→CAG) | otsA ← | trehalose‑6‑phosphate synthase |
| RA | 2,071,308 | G→T | intergenic (+97/‑9) | yeeP → / → isrC | pseudogene, CP4‑44 prophage, 50S ribosome‑binding GTPase family,Phage or Prophage Related, putative histone/novel sRNA, CP4‑44, putative prophage remnant |
| RA | 2,073,225 | T→C | W563R (TGG→CGG) | flu → | CP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| RA | 2,144,279 | T→C | S338S (AGT→AGC) | 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 | 2,297,084 | C→T | Q187Q (CAG→CAA) | ccmA ← | heme export ABC transporter ATPase |
| RA | 2,401,103 | G→A | T151T (ACC→ACT) | nuoF ← | NADH:ubiquinone oxidoreductase, chain F |
| RA | 2,464,156 | T→C | intergenic (+86/+96) | yfdF → / ← mlaA | uncharacterized protein/ABC transporter maintaining OM lipid asymmetry, OM lipoprotein component |
| RA | 2,513,564 | T→C | S175P (TCC→CCC) | nupC → | nucleoside (except guanosine) transporter |
| 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 | 2,937,802 | A→G | D112G (GAC→GGC) | fucK → | L‑fuculokinase |
| RA | 3,001,304 | (G)7→8 | coding (960/2259 nt) | xdhA → | xanthine dehydrogenase, molybdenum binding subunit |
| RA | 3,139,583 | G→A | R286H (CGT→CAT) | yghU → | putative S‑transferase |
| RA | 3,204,189 | G→A | intergenic (‑58/+32) | bacA ← / ← folB | undecaprenyl pyrophosphate phosphatase/dihydroneopterin aldolase and dihydroneopterin triphosphate 2'‑epimerase |
| RA | 3,271,600 | (C)5→6 | coding (171/1146 nt) | garK ← | glycerate kinase I |
| RA | 3,350,184 | (C)7→8 | coding (276/654 nt) | elbB ← | isoprenoid biosynthesis protein with amidotransferase‑like domain |
| RA | 3,366,953 | G→A | G10R (GGA→AGA) | yhcF → | putative transcriptional regulator |
| RA | 3,457,094 | A→G | I240V (ATC→GTC) | gspD → | general secretory pathway component, cryptic |
| RA | 3,464,087 | A→T | I56F (ATC→TTC) | gspL → | general secretory pathway component, cryptic |
| RA | 3,490,191 | C→T | intergenic (‑11/+75) | argD ← / ← pabA | bifunctional acetylornithine aminotransferase and succinyldiaminopimelate aminotransferase/aminodeoxychorismate synthase, subunit II |
| RA | 3,535,392 | C→T | P159P (CCG→CCA) | envZ ← | sensory histidine kinase in two‑component regulatory system with OmpR |
| 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 | 3,561,426 | (G)5→6 | coding (27/831 nt) | glpG ← | rhomboid intramembrane serine protease |
| RA | 3,702,561 | A→T | I103N (ATC→AAC) | dppF ← | dipeptide/heme ABC transporter ATPas |
| 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 | 3,858,248 | T→C | T53A (ACG→GCG) | yidJ ← | sulfatase/phosphatase superfamily protein |
| 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 | 4,060,280 | (T)9→8 | intergenic (+50/‑167) | typA → / → yihL | GTP‑binding protein/putative DNA‑binding transcriptional regulator |
| RA | 4,188,572 | C→T | R1075C (CGT→TGT) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,281,472 | A→G | E498G (GAG→GGG) | yjcE → | putative cation/proton antiporter |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,459,820 | A→G | pseudogene (331/366 nt) | cybC → | pseudogene, truncated cytochrome b562, cytochrome b(562) |
| RA | 4,489,696 | A→G | L123P (CTG→CCG) | yjgR ← | DUF853 family protein with NTPase fold |
| 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 |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 807329 | 810371 | 3043 | 14 [10] | [9] 11 | ybhB–[bioB] | ybhB, bioA, [bioB] |
| * | * | ÷ | NC_000913 | 2857135 | 2859630 | 2496 | 12 [10] | [10] 11 | mutS | methyl‑directed mismatch repair protein |
| * | * | ÷ | NC_000913 | 3423770–3424230 | 3424544–3424242 | 13–775 | 11 [10] | [9] 12 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 380012 | 18 (0.360) | 24 (0.450) +GGG |
17/200 | 1.4 | 56.6% | intergenic (‑131/+57) | frmR/yaiO | regulator protein that represses frmRAB operon/outer membrane protein |
| ? | NC_000913 | 380013 = | 18 (0.330) | intergenic (‑132/+56) | frmR/yaiO | regulator protein that represses frmRAB operon/outer membrane protein | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 56 (1.070) | 40/218 | 0.2 | 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 | |||||