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 | 190,778 | (G)5→6 | intergenic (+179/‑79) | rpsB → / → tsf | 30S ribosomal subunit protein S2/translation elongation factor EF‑Ts |
| RA | 251,799 | A→G | E301G (GAG→GGG) | dinB → | DNA polymerase IV |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 324,641 | C→T | intergenic (+188/+55) | ykgG → / ← ykgH | LutC family protein, putative electron transport chain YkgEFG component/putative inner membrane protein |
| RA | 352,986 | A→G | N94S (AAC→AGC) | prpE → | propionate‑‑CoA ligase |
| RA | 365,380 | A→G | L309P (CTC→CCC) | lacZ ← | beta‑D‑galactosidase |
| RA | 573,440 | C→T | R24C (CGC→TGC) | rusA → | DLP12 prophage, endonuclease RUS |
| RA | 638,399 | A→G | Y59H (TAC→CAC) | dsbG ← | thiol:disulfide interchange protein, periplasmic |
| RA | 638,619 | A→G | intergenic (‑46/‑326) | dsbG ← / → ahpC | thiol:disulfide interchange protein, periplasmic/alkyl hydroperoxide reductase, C22 subunit |
| RA | 746,842 | T→C | S310G (AGC→GGC) | abrB ← | regulator of aidB expression, inner membrane protein |
| RA | 783,866 | C→T | S234L (TCA→TTA) | pnuC → | nicotinamide riboside transporter |
| RA | 791,349 | A→G | V236A (GTA→GCA) | galE ← | UDP‑galactose‑4‑epimerase |
| RA | 1,118,516 | G→A | R177R (CGC→CGT) | yceJ ← | putative cytochrome b561 |
| RA | 1,121,934 | A→G | I225T (ATC→ACC) | pyrC ← | dihydro‑orotase |
| RA | 1,190,263 | A→G | L62P (CTG→CCG) | phoP ← | response regulator in two‑component regulatory system with PhoQ |
| RA | 1,225,697 | T→C | I128M (ATA→ATG) | minC ← | inhibitor of FtsZ ring polymerization |
| RA | 1,287,826 | C→T | A267T (GCA→ACA) | purU ← | formyltetrahydrofolate hydrolase |
| 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 | 1,412,027 | T→C | I403M (ATA→ATG) | intR ← | Rac prophage, integrase |
| RA | 1,458,617 | A→G | A118A (GCA→GCG) | paaG → | 1,2‑epoxyphenylacetyl‑CoA isomerase, oxepin‑CoA‑forming |
| RA | 1,460,048 | C→T | A332V (GCG→GTG) | paaH → | 3‑hydroxyadipyl‑CoA dehydrogenase, NAD+‑dependent |
| RA | 1,503,221 | A→G | pseudogene (429/432 nt) | insP ← | pseudogene, IS609 transposase A,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon related |
| RA | 1,581,323 | G→A | T401I (ACA→ATA) | ydeN ← | putative Ser‑type periplasmic non‑aryl sulfatase |
| RA | 1,595,427 | A→G | pseudogene (2561/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,629,649 | A→G | L422P (CTG→CCG) | ydfI ← | putative NAD‑dependent D‑mannonate oxidoreductase |
| RA | 1,667,344 | T→C | *407* (TAA→TAG) | mlc ← | glucosamine anaerobic growth regulon transcriptional repressor, autorepressor |
| RA | 1,806,541 | A→T | I58F (ATC→TTC) | pfkB → | 6‑phosphofructokinase II |
| RA | 1,812,173 | T→C | L414L (TTA→CTA) | ydjN → | putative transporter |
| RA | 1,836,204 | C→T | T44T (ACC→ACT) | ynjB → | putative ABC transporter periplasmic binding protein |
| 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 | 2,073,094 | T→C | L519P (CTG→CCG) | flu → | CP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| 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 | 2,189,791 | A→G | Y374H (TAT→CAT) | yehB ← | putative outer membrane protein |
| RA | 2,248,780 | C→T | R280Q (CGG→CAG) | yeiE ← | putative DNA‑binding transcriptional regulator |
| RA | 2,311,756 | A→G | S332P (TCC→CCC) | ompC ← | outer membrane porin protein C |
| RA | 2,319,725 | T→C | E51G (GAA→GGA) | rcsC ← | hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| RA | 2,401,103 | G→A | T151T (ACC→ACT) | nuoF ← | NADH:ubiquinone oxidoreductase, chain F |
| RA | 2,523,413 | T→C | T191T (ACA→ACG) | xapB ← | xanthosine transporter |
| RA | 2,602,161 | Δ1 bp | coding (344/2019 nt) | hyfB → | hydrogenase 4, membrane subunit |
| RA | 2,682,157 | (C)7→8 | coding (589/3282 nt) | yphG ← | DUF4380 domain‑containing TPR repeat protein |
| RA | 2,734,535 | T→C | E167G (GAG→GGG) | 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 | 2,937,802 | A→G | D112G (GAC→GGC) | fucK → | L‑fuculokinase |
| RA | 2,977,182 | Δ1 bp | coding (584/1032 nt) | galR → | galactose‑inducible d‑galactose regulon transcriptional repressor, autorepressor |
| RA | 3,001,304 | (G)7→8 | coding (960/2259 nt) | xdhA → | xanthine dehydrogenase, molybdenum binding subunit |
| RA | 3,051,507 | G→A | L271L (CTG→TTG) | ubiI ← | 2‑octaprenylphenol hydroxylase, FAD‑dependent |
| RA | 3,139,583 | G→A | R286H (CGT→CAT) | yghU → | putative S‑transferase |
| RA | 3,172,259 | G→A | intergenic (‑48/‑271) | ygiZ ← / → mdaB | inner membrane protein/NADPH quinone reductase |
| RA | 3,216,464 | G→A | R10C (CGC→TGC) | yqjH ← | putative siderophore interacting protein |
| RA | 3,245,522 | G→A | G100D (GGC→GAC) | exuT → | hexuronate transporter |
| RA | 3,271,600 | (C)5→6 | coding (171/1146 nt) | garK ← | glycerate kinase I |
| RA | 3,346,060 | A→G | E448E (GAA→GAG) | rpoN → | RNA polymerase, sigma 54 (sigma N) factor |
| 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 | 3,495,153 | T→C | G381G (GGT→GGC) | nirB → | nitrite reductase, large subunit, NAD(P)H‑binding |
| 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 | 3,748,181 | G→A | A366A (GCG→GCA) | lyxK → | L‑xylulose kinase |
| RA | 3,785,021 | (G)6→7 | intergenic (‑6/‑239) | yibN ← / → gpmM | putative rhodanese‑related sulfurtransferase/phosphoglycero mutase III, cofactor‑independent |
| 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 | 3,901,765 | 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 | 4,136,860 | A→G | T251T (ACA→ACG) | yijE → | EamA‑like transporter family protein |
| RA | 4,182,791 | A→G | D516G (GAC→GGC) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,186,296 | T→A | I316N (ATC→AAC) | 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 | 4,351,093 | G→A | G190G (GGC→GGT) | dcuS ← | sensory histidine kinase in two‑component regulatory system with DcuR, regulator of anaerobic fumarate respiration |
| RA | 4,385,643 | T→C | L84S (TTA→TCA) | yjeN → | uncharacterized protein |
| RA | 4,457,798 | T→C | E23G (GAA→GGA) | yjgA ← | ribosome‑associated UPF0307 family protein |
| RA | 4,488,579 | (C)7→8 | coding (1485/1503 nt) | yjgR ← | DUF853 family protein with NTPase fold |
| RA | 4,490,935 | A→G | L69L (TTG→CTG) | idnR ← | transcriptional repressor, 5‑gluconate‑binding |
| RA | 4,533,223 | A→G | intergenic (‑40/+16) | yjhP ← / ← yjhQ | putative methyltransferase/GNAT family putative N‑acetyltransferase |
| 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 | 807340 | 810368 | 3029 | 5 [3] | [4] 6 | ybhB–[bioB] | ybhB, bioA, [bioB] |
| * | * | ÷ | NC_000913 | 1640976 | 1641029 | 54 | 8 [4] | [1] 16 | essQ/cspB | Qin prophage, putative S lysis protein/Qin prophage, cold shock protein |
| * | * | ÷ | NC_000913 | 2470198 | 2470281 | 84 | 5 [1] | [4] 8 | gtrS | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| * | * | ÷ | NC_000913 | 2857130 | 2859608 | 2479 | 6 [4] | [0] 7 | mutS | methyl‑directed mismatch repair protein |
| * | * | ÷ | NC_000913 | 2995170 | 2995271 | 102 | 5 [3] | [3] 5 | ygeK/ygeN | pseudogene, response regulator family, part of T3SS PAI ETT2 remnant, putative 2‑component transcriptional regulator/pseudogene, orgB family, part of T3SS PAI ETT2 remnant |
| * | * | ÷ | NC_000913 | 3423767–3424234 | 3424524–3424238 | 5–758 | 6 [4] | [4] 5 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| * | * | ÷ | NC_000913 | 3499402 | 3499436 | 35 | 5 [3] | [4] 18 | cysG/yhfL | fused siroheme synthase 1,3‑dimethyluroporphyriongen III dehydrogenase and siroheme ferrochelatase/uroporphyrinogen methyltransferase/small lipoprotein |
| * | * | ÷ | NC_000913 | 3793684 | 3793746 | 63 | 5 [4] | [3] 13 | yibB/hldD | YibB family protein, function unknown/ADP‑L‑glycero‑D‑mannoheptose‑6‑epimerase, NAD(P)‑binding |
| * | * | ÷ | NC_000913 | 4326047–4326087 | 4326173–4326089 | 3–127 | 5 [4] | [4] 5 | yjdN/yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 34 (0.940) | 9 (0.290) | 9/192 | 1.6 | 24.6% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 26 (0.840) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||