mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 310 | (T)9→10 | intergenic (+55/‑27) | thrL → / → thrA | thr operon leader peptide/fused aspartate kinase/homoserine dehydrogenase 1 |
| RA | 746 | T→C | V137A (GTA→GCA) | thrA → | fused aspartate kinase/homoserine dehydrogenase 1 |
| RA | 30,689 | G→A | A347T (GCA→ACA) | carA → | carbamoyl phosphate synthetase subunit alpha |
| RA | 62,358 | C→T | A303T (GCA→ACA) | rapA ← | RNA polymerase‑binding ATPase and RNAP recycling factor |
| RA | 65,698 | T→C | D28G (GAC→GGC) | polB ← | DNA polymerase II |
| RA | 72,644 | C→T | G95E (GGG→GAG) | thiQ ← | thiamine ABC transporter ATP binding subunit |
| RA | 75,607 | A→G | intergenic (‑127/+37) | thiB ← / ← sgrR | thiamine ABC transporter periplasmic binding protein/DNA‑binding transcriptional dual regulator SgrR |
| RA | 84,655 | A→G | V96V (GTA→GTG) | leuO → | DNA‑binding transcriptional dual regulator LeuO |
| RA | 88,279 | A→G | E84E (GAA→GAG) | cra → | DNA‑binding transcriptional dual regulator Cra |
| RA | 100,328 | G→A | A229T (GCG→ACG) | murG → | N‑acetylglucosaminyl transferase |
| RA | 115,813 | A→G | G429G (GGT→GGC) | hofB ← | T2SSE family protein |
| RA | 122,534 | A→G | N148S (AAC→AGC) | pdhR → | DNA‑binding transcriptional dual regulator PdhR |
| RA | 128,530 | T→C | F207L (TTC→CTC) | lpd → | lipoamide dehydrogenase |
| RA | 134,603 | G→A | V72V (GTG→GTA) | yacL → | UPF0231 family protein YacL |
| RA | 155,212 | T→C | D72G (GAC→GGC) | htrE ← | putative fimbrial usher protein HtrE |
| RA | 177,927 | A→G | V179A (GTA→GCA) | btuF ← | vitamin B12 ABC transporter periplasmic binding protein |
| RA | 234,901 | T→C | L29P (CTG→CCG) | yafS → | putative S‑adenosyl‑L‑methionine‑dependent methyltransferase |
| RA | 255,174 | (C)6→7 | coding (543/1458 nt) | pepD ← | peptidase D |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 273,814 | T→C | I323T (ATC→ACC) | ykfC → | CP4‑6 prophage; PF00078 domain‑containing protein YkfC |
| RA | 298,429 | A→G | Y100H (TAT→CAT) | paoD ← | molybdenum cofactor insertion chaperone for PaoABC |
| RA | 298,818 | A→G | V706A (GTG→GCG) | paoC ← | aldehyde dehydrogenase: molybdenum cofactor‑binding subunit |
| RA | 308,054 | (C)7→8 | coding (1279/2526 nt) | ecpC ← | putative fimbrial usher protein EcpC |
| RA | 339,529 | A→G | N402S (AAC→AGC) | yahG → | DUF1116 domain‑containing protein YahG |
| RA | 365,156 | T→C | N384D (AAC→GAC) | lacZ ← | beta‑galactosidase |
| RA | 380,022 | (G)10→11 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 384,281 | A→G | S112S (TCT→TCC) | yaiS ← | putative deacetylase YaiS |
| RA | 394,042 | A→G | pseudogene (1073/1449 nt) | yaiT → | putative autotransporter YaiT |
| RA | 396,114 | A→G | G58G (GGT→GGC) | ampH ← | peptidoglycan DD‑carboxypeptidase/peptidoglycan DD‑endopeptidase |
| RA | 401,670 | T→C | intergenic (+24/‑77) | iraP → / → phoA | anti‑adaptor protein for sigma(S) stabilization/alkaline phosphatase |
| RA | 476,542 | A→G | noncoding (95/114 nt) | ffs → | signal recognition particle 4.5S RNA |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 529,055 | (T)8→9 | pseudogene (416/491 nt) | ybbD → | putative uncharacterized protein YbbD |
| RA | 595,224 | G→A | P74S (CCG→TCG) | cusR ← | DNA‑binding transcriptional activator CusR |
| RA | 669,398 | Δ1 bp | coding (510/612 nt) | cobC ← | putative adenosylcobalamin phosphatase/alpha‑ribazole phosphatase |
| RA | 717,125 | (G)6→7 | coding (1141/1320 nt) | potE ← | putrescine:H(+) symporter/putrescine:ornithine antiporter PotE |
| RA | 732,401 | A→G | D940G (GAC→GGC) | rhsC → | rhs element protein RhsC |
| RA | 733,643 | T→C | F1354S (TTC→TCC) | rhsC → | rhs element protein RhsC |
| RA | 770,985 | (T)5→4 | intergenic (+374/‑473) | mngB → / → cydA | alpha‑mannosidase/cytochrome bd‑I ubiquinol oxidase subunit I |
| RA | 789,580 | C→T | E134K (GAA→AAA) | galK ← | galactokinase |
| RA | 797,241 | C→T | Q230* (CAA→TAA) | modC → | molybdate ABC transporter ATP binding subunit |
| RA | 812,985 | T→C | intergenic (+38/‑541) | bioD → / → uvrB | dethiobiotin synthetase/excision nuclease subunit B |
| RA | 852,439 | T→C | L53L (CTA→CTG) | opgE ← | phosphoethanolamine transferase |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 899,900 | C→T | A226T (GCA→ACA) | artJ ← | L‑arginine ABC transporter periplasmic binding protein |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 950,098 | (A)7→8 | coding (431/591 nt) | ycaK → | putative NAD(P)H‑dependent oxidoreductase YcaK |
| RA | 989,615 | A→G | Y248H (TAT→CAT) | pncB ← | nicotinate phosphoribosyltransferase |
| RA | 999,141 | A→G | T218A (ACC→GCC) | elfD → | putative fimbrial chaperone ElfD |
| RA | 1,002,224 | (G)7→6 | coding (418/1071 nt) | elfG → | putative fimbrial‑like adhesin protein |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,052,491 | G→A | A291V (GCC→GTC) | yccM ← | putative 4Fe‑4S membrane protein |
| RA | 1,080,256 | G→A | A318T (GCG→ACG) | putP → | proline:Na(+) symporter |
| RA | 1,110,873 | C→T | T4I (ACA→ATA) | opgH → | osmoregulated periplasmic glucans (OPGs) biosynthesis protein H |
| RA | 1,126,649 | C→T | H165Y (CAT→TAT) | yceH → | DUF480 domain‑containing protein YceH |
| RA | 1,131,872 | A→G | T7A (ACC→GCC) | flgD → | flagellar biosynthesis, initiation of hook assembly |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,154,503 | Δ1 bp | coding (392/1023 nt) | mltG → | endolytic murein transglycosylase |
| RA | 1,164,550 | T→C | G152G (GGT→GGC) | nagZ → | beta‑N‑acetylhexosaminidase |
| RA | 1,172,172 | G→A | P598L (CCG→CTG) | mfd ← | transcription‑repair coupling factor |
| RA | 1,172,514 | A→G | V484A (GTC→GCC) | mfd ← | transcription‑repair coupling factor |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,243,627 | Δ1 bp | coding (448/612 nt) | emtA → | lytic murein transglycosylase E |
| RA | 1,263,632 | (G)5→4 | intergenic (‑132/‑82) | lolB ← / → hemA | outer membrane lipoprotein LolB/glutamyl‑tRNA reductase |
| RA | 1,266,530 | T→C | V146A (GTC→GCC) | prmC → | protein‑(glutamine‑N(5)) methyltransferase |
| RA | 1,270,545 | G→T | intergenic (+85/+204) | rdlC → / ← chaA | small regulatory antisense RNA RdlC/Na(+)/K(+):H(+) antiporter ChaA |
| RA | 1,272,125 | T→C | Y3H (TAT→CAT) | chaB → | putative cation transport regulator ChaB |
| RA | 1,277,410 | T→C | D70G (GAC→GGC) | narX ← | sensory histidine kinase NarX |
| RA | 1,298,959 | T→C | V121A (GTG→GCG) | ychE → | putative inner membrane protein |
| RA | 1,310,751 | T→C | T39A (ACA→GCA) | yciI ← | protein YciI |
| RA | 1,334,153 | C→T | T100M (ACG→ATG) | cysB → | DNA‑binding transcriptional dual regulator CysB |
| RA | 1,357,342 | A→G | intergenic (‑232/+81) | sapA ← / ← ymjA | putative periplasmic binding protein SapA/DUF2543 domain‑containing protein YmjA |
| RA | 1,365,094 | A→G | Y288C (TAC→TGC) | puuB → | gamma‑glutamylputrescine oxidase |
| RA | 1,413,413 | A→G | Y14H (TAC→CAC) | xisR ← | Rac prophage; excisionase |
| RA | 1,472,368 | A→G | pseudogene (1850/3495 nt) | ydbA → | putative outer membrane protein, N‑terminal fragment |
| RA | 1,475,398 | T→C | S85S (AGT→AGC) | ydbD → | DUF2773 domain‑containing protein YdbD |
| RA | 1,510,788 | (A)8→9 | coding (786/1407 nt) | ydcR → | fused putative DNA‑binding transcriptional regulator/putative aminotransferase YdcR |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,541,861 | A→G | W244R (TGG→CGG) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,568,308 | A→G | G172G (GGT→GGC) | yddW ← | putative lipoprotein YddW |
| RA | 1,595,543 | A→G | pseudogene (2544/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,603,810 | T→C | G264G (GGT→GGC) | lsrC → | Autoinducer‑2 ABC transporter membrane subunit LsrC |
| RA | 1,617,459 | C→T | T144T (ACC→ACT) | ydeA → | L‑arabinose exporter |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,648,247 | A→G | D105G (GAT→GGT) | dicA → | DNA‑binding transcriptional dual regulator DicA |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,712,712 | (T)6→5 | intergenic (+554/‑57) | nth → / → dtpA | endonuclease III/dipeptide/tripeptide:H(+) symporter DtpA |
| RA | 1,724,478 | (G)6→7 | coding (178/522 nt) | sodC ← | superoxide dismutase (Cu‑Zn) |
| RA | 1,761,725 | T→C | T23A (ACA→GCA) | sufD ← | Fe‑S cluster scaffold complex subunit SufD |
| RA | 1,768,441 | (G)6→5 | coding (245/3057 nt) | ydiJ ← | putative FAD‑linked oxidoreductase |
| RA | 1,771,123 | T→C | V18A (GTG→GCG) | ydiM → | putative exporter YdiM |
| RA | 1,799,071 | T→A | intergenic (‑129/+155) | pheS ← / ← pheM | phenylalanine‑‑tRNA ligase subunit alpha/pheST‑ihfA operon leader peptide |
| RA | 1,873,384 | A→G | K448K (AAA→AAG) | dgcJ → | putative diguanylate cyclase DgcJ |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,886,585 | G→A | V247V (GTG→GTA) | yeaX → | carnitine monooxygenase subunit YeaX |
| RA | 1,919,648 | T→C | T713T (ACT→ACC) | yebT → | intermembrane transport protein YebT |
| RA | 1,920,784 | T→C | F188L (TTC→CTC) | rsmF → | 16S rRNA m(5)C1407 methyltransferase |
| RA | 1,925,000 | (T)6→7 | intergenic (‑31/‑108) | yobA ← / → holE | CopC domain‑containing protein/DNA polymerase III subunit theta |
| RA | 1,929,001 | T→C | intergenic (‑162/+47) | ptrB ← / ← yebE | oligopeptidase B/conserved inner membrane protein YebE |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 1,985,515 | G→A | A205V (GCA→GTA) | araF ← | arabinose ABC transporter periplasmic binding protein |
| RA | 2,057,676 | (C)7→8 | intergenic (+102/+351) | yeeN → / ← asnW | putative transcriptional regulator YeeN/tRNA‑Asn |
| RA | 2,096,209 | G→A | V122V (GTG→GTA) | hisF → | imidazole glycerol phosphate synthase subunit HisF |
| RA | 2,113,672 | G→A | A219V (GCC→GTC) | galF ← | UTP:glucose‑1‑phosphate uridylyltransferase, low activity |
| RA | 2,114,380 | (T)7→6 | intergenic (‑53/+122) | galF ← / ← wcaM | UTP:glucose‑1‑phosphate uridylyltransferase, low activity/putative colanic acid biosynthesis protein WcaM |
| RA | 2,124,416 | T→C | K35K (AAA→AAG) | cpsB ← | mannose‑1‑phosphate guanylyltransferase |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,200,454 | (A)8→7 | coding (176/3633 nt) | yehI → | DUF4132 domain‑containing protein YehI |
| RA | 2,202,995 | G→A | S906N (AGC→AAC) | yehI → | DUF4132 domain‑containing protein YehI |
| RA | 2,228,774 | T→C | intergenic (‑16/‑208) | mdtQ ← / → yohP | putative multidrug resistance outer membrane protein MdtQ/putative membrane protein YohP |
| RA | 2,304,077 | T→C | V58A (GTA→GCA) | eco → | serine protease inhibitor ecotin |
| RA | 2,309,596 | Δ1 bp | coding (810/1065 nt) | ada ← | DNA‑binding transcriptional dual regulator/DNA repair protein Ada |
| RA | 2,313,965 | Δ1 bp | coding (478/2673 nt) | rcsD → | RcsD phosphotransferase |
| RA | 2,328,828 | C→T | E324K (GAA→AAA) | yfaQ ← | tandem DUF2300 domain‑containing protein YfaQ |
| RA | 2,339,206 | T→C | D72G (GAC→GGC) | gyrA ← | DNA gyrase subunit A |
| RA | 2,352,253 | T→C | Y41C (TAC→TGC) | glpT ← | sn‑glycerol 3‑phosphate:phosphate antiporter |
| RA | 2,394,188 | Δ1 bp | coding (859/1842 nt) | nuoL ← | NADH:quinone oxidoreductase subunit L |
| RA | 2,396,354 | A→G | Y33H (TAC→CAC) | nuoI ← | NADH:quinone oxidoreductase subunit I |
| RA | 2,407,333 | (A)7→6 | intergenic (‑692/‑228) | lrhA ← / → alaA | DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA |
| RA | 2,412,143 | T→C | Y151C (TAC→TGC) | yfbU ← | UPF0304 family protein YfbU |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,453,508 | G→A | pseudogene (1494/2646 nt) | yfcU ← | putative outer membrane usher protein YfcU |
| JC | 2,462,889 | (C)9→12 | intergenic (+243/‑123) | fadL → / → yfdF | long‑chain fatty acid outer membrane channel/bacteriophage T2 receptor/protein YfdF |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,539,741 | T→C | E358E (GAA→GAG) | cysA ← | sulfate/thiosulfate ABC transporter ATP binding subunit |
| RA | 2,572,965 | T→C | I181V (ATC→GTC) | eutD ← | phosphate acetyltransferase EutD |
| RA | 2,602,017 | (C)7→8 | coding (200/2019 nt) | hyfB → | hydrogenase 4 component B |
| RA | 2,673,991 | A→G | F233S (TTC→TCC) | yphB ← | putative aldose 1‑epimerase YphB |
| RA | 2,678,695 | T→C | M225V (ATG→GTG) | yphF ← | putative ABC transporter periplasmic binding protein YphF |
| RA | 2,705,998 | G→A | T376I (ACC→ATC) | lepA ← | elongation factor 4 |
| RA | 2,716,526 | G→A | intergenic (‑77/‑228) | grcA ← / → ung | stress‑induced alternate pyruvate formate‑lyase subunit/uracil‑DNA glycosylase |
| RA | 2,718,698 | T→C | intergenic (‑170/‑37) | yfiF ← / → trxC | putative methyltransferase/reduced thioredoxin 2 |
| RA | 2,719,486 | T→C | R88R (CGT→CGC) | yfiP → | conserved protein YfiP |
| RA | 2,741,073 | +A | coding (78/1071 nt) | aroF ← | 3‑deoxy‑7‑phosphoheptulonate synthase, Tyr‑sensitive |
| RA | 2,766,360 | A→G | D148G (GAC→GGC) | rnlA → | CP4‑57 prophage; RNase LS, toxin of the RnlAB toxin‑antitoxin system |
| RA | 2,767,445 | (C)7→8 | intergenic (+90/‑265) | rnlB → / → yfjP | CP4‑57 prophage; antitoxin RnlB/CP4‑57 prophage; putative GTP‑binding protein YfjP |
| RA | 2,773,113 | C→T | pseudogene (70/1016 nt) | yfjV ← | CP4‑57 prophage; putative arsenite transporter, N‑terminal fragment |
| RA | 2,778,930 | (C)6→5 | coding (3797/4581 nt) | ypjA ← | adhesin‑like autotransporter YpjA |
| RA | 2,802,472 | T→C | A375A (GCT→GCC) | nrdE → | ribonucleoside‑diphosphate reductase 2 subunit alpha |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,824,038 | A→G | S103S (AGT→AGC) | pncC ← | NMN aminohydrolase |
| RA | 2,844,820 | A→G | V551A (GTG→GCG) | hycE ← | formate hydrogenlyase subunit HycE |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,867,956 | G→A | G266G (GGC→GGT) | nlpD ← | murein hydrolase activator NlpD |
| RA | 2,880,579 | (A)7→8 | coding (470/675 nt) | casD ← | type I‑E CRISPR system Cascade subunit CasD |
| RA | 2,880,898 | T→C | T51A (ACT→GCT) | casD ← | type I‑E CRISPR system Cascade subunit CasD |
| RA | 2,910,723 | A→G | intergenic (‑38/+33) | mazG ← / ← mazF | nucleoside triphosphate pyrophosphohydrolase/endoribonuclease toxin MazF |
| RA | 2,925,012 | T→C | H90R (CAC→CGC) | syd ← | SecY‑interacting protein |
| RA | 2,940,984 | (G)5→6 | coding (260/1101 nt) | rlmM ← | 23S rRNA 2'‑O‑ribose C2498 methyltransferase |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,952,692 | T→C | A1104A (GCA→GCG) | recB ← | exodeoxyribonuclease V subunit RecB |
| RA | 2,980,296 | +C | coding (340/693 nt) | ygeA ← | amino acid racemase |
| RA | 2,981,901 | (C)5→6 | coding (282/1419 nt) | araE ← | arabinose:H(+) symporter |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,158,773 | A→G | A49A (GCA→GCG) | yqhH → | lipoprotein YqhH |
| RA | 3,188,538 | C→T | pseudogene (1107/2434 nt) | yqiG → | putative outer membrane usher protein YqiG |
| RA | 3,190,744 | A→G | Y38C (TAC→TGC) | yqiI → | putative fimbrial protein YqiI |
| RA | 3,207,828 | G→A | W153* (TGG→TAG) | ttdB → | L(+)‑tartrate dehydratase subunit beta |
| RA | 3,237,712 | G→A | Q134Q (CAG→CAA) | ygjR → | putative oxidoreductase YgjR |
| RA | 3,244,741 | T→C | M1M (ATG→GTG) † | uxaC ← | D‑glucoronate/D‑galacturonate isomerase |
| RA | 3,250,172 | G→A | W32* (TGG→TGA) | yqjK → | conserved protein YqjK |
| RA | 3,254,967 | A→G | T217A (ACG→GCG) | yhaK → | bicupin‑related protein |
| RA | 3,268,304 | (C)6→7 | coding (451/540 nt) | yhaB → | protein YhaB |
| RA | 3,300,238 | T→C | S91S (AGT→AGC) | yhbQ → | DNA damage response nuclease YhbQ |
| RA | 3,318,389 | T→C | intergenic (‑100/‑248) | metY ← / → argG | tRNA‑Met/argininosuccinate synthetase |
| RA | 3,332,680 | (C)6→7 | coding (56/966 nt) | yhbE ← | inner membrane protein YhbE |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,371,435 | T→C | G380G (GGA→GGG) | nanT ← | N‑acetylneuraminate:H(+) symporter |
| RA | 3,374,484 | G→A | G2G (GGC→GGT) | nanR ← | DNA‑binding transcriptional dual regulator NanR |
| RA | 3,375,991 | T→C | F375L (TTT→CTT) | dcuD → | putative transporter DcuD |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,411,037 | C→T | A253V (GCA→GTA) | dusB → | tRNA‑dihydrouridine synthase B |
| RA | 3,433,448 | A→G | V38A (GTA→GCA) | smf ← | protein Smf |
| RA | 3,443,769 | T→C | E110G (GAG→GGG) | secY ← | Sec translocon subunit SecY |
| RA | 3,451,262 | C→T | E35K (GAA→AAA) | rplB ← | 50S ribosomal subunit protein L2 |
| RA | 3,456,803 | (C)6→7 | coding (427/1953 nt) | gspD → | Type II secretion system protein GspD |
| RA | 3,495,653 | T→C | L548P (CTG→CCG) | nirB → | nitrite reductase catalytic subunit NirB |
| RA | 3,501,834 | T→C | H189H (CAT→CAC) | frlB → | fructoselysine 6‑phosphate deglycase |
| RA | 3,540,380 | T→C | V73A (GTT→GCT) | feoA → | ferrous iron transport protein A |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,565,382 | A→G | Y400Y (TAT→TAC) | glgP ← | glycogen phosphorylase |
| RA | 3,591,352 | G→A | A325V (GCG→GTG) | ugpB ← | sn‑glycerol 3‑phosphate ABC transporter periplasmic binding protein |
| RA | 3,603,835 | T→C | I137V (ATT→GTT) | ftsY ← | signal recognition particle receptor |
| RA | 3,629,470 | (T)5→6 | coding (69/2736 nt) | rbbA ← | ribosome‑associated ATPase |
| RA | 3,637,817 | T→C | V59A (GTA→GCA) | pitA → | metal phosphate:H(+) symporter PitA |
| RA | 3,649,771 | (C)5→6 | coding (837/1290 nt) | arsB → | arsenite/antimonite:H(+) antiporter |
| RA | 3,728,118 | (C)8→9 | coding (1254/1455 nt) | xylB ← | xylulokinase |
| RA | 3,786,297 | T→C | G346G (GGT→GGC) | gpmM → | 2,3‑bisphosphoglycerate‑independent phosphoglycerate mutase |
| RA | 3,808,983 | G→A | L148L (CTG→CTA) | waaA → | KDO transferase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,838,343 | C→T | S32S (AGC→AGT) | yicL → | putative inner membrane protein |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,940,954 | A→G | V125A (GTT→GCT) | yieP ← | putative transcriptional regulator YieP |
| RA | 4,011,402 | T→C | R109R (CGT→CGC) | bioP → | biotin transporter |
| RA | 4,018,973 | A→G | N40S (AAT→AGT) | ubiE → | bifunctional 2‑octaprenyl‑6‑methoxy‑1,4‑benzoquinone methylase and S‑adenosylmethionine:2‑DMK methyltransferase |
| RA | 4,023,265 | T→C | L177P (CTG→CCG) | tatC → | twin arginine protein translocation system ‑ TatC protein |
| RA | 4,138,433 | T→C | A201A (GCA→GCG) | gldA ← | L‑1,2‑propanediol dehydrogenase/glycerol dehydrogenase |
| RA | 4,181,024 | A→G | intergenic (+99/‑221) | rplL → / → rpoB | 50S ribosomal subunit protein L12/RNA polymerase subunit beta |
| RA | 4,200,096 | A→G | intergenic (+2/‑185) | yjaG → / → hupA | conserved protein YjaG/DNA‑binding protein HU‑alpha |
| RA | 4,202,187 | C→T | P88S (CCG→TCG) | zraS → | sensory histidine kinase ZraS |
| RA | 4,206,742 | T→C | N264S (AAC→AGC) | purH ← | bifunctional AICAR transformylase/IMP cyclohydrolase |
| RA | 4,234,871 | A→G | T372A (ACT→GCT) | pgi → | glucose‑6‑phosphate isomerase |
| RA | 4,237,358 | C→T | S154S (AGC→AGT) | yjbG → | capsule biosynthesis GfcC family protein YjbG |
| RA | 4,276,165 | A→G | Y232C (TAT→TGT) | pdeC → | c‑di‑GMP phosphodiesterase PdeC |
| RA | 4,286,716 | A→G | V219A (GTA→GCA) | acs ← | acetyl‑CoA synthetase (AMP‑forming) |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,307,299 | (G)5→6 | coding (501/930 nt) | alsK ← | D‑allose kinase |
| RA | 4,339,091 | T→C | K477K (AAA→AAG) | adiA ← | arginine decarboxylase, degradative |
| RA | 4,344,573 | A→G | Q402R (CAG→CGG) | melB → | melibiose:H(+)/Na(+)/Li(+) symporter |
| RA | 4,395,669 | A→G | T29A (ACC→GCC) | tsaE → | N(6)‑L‑threonylcarbamoyladenine synthase, TsaE subunit |
| RA | 4,422,914 | A→G | E23E (GAA→GAG) | ulaE → | L‑ribulose‑5‑phosphate 3‑epimerase UlaE |
| RA | 4,437,443 | A→G | Y230C (TAC→TGC) | cysQ → | 3'(2'),5'‑bisphosphate nucleotidase |
| RA | 4,441,374 | A→G | intergenic (‑159/+164) | ytfL ← / ← msrA | putative inner membrane protein/methionine sulfoxide reductase A |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,452,352 | G→A | G432D (GGC→GAC) | ytfR → | galactofuranose ABC transporter putative ATP binding subunit |
| RA | 4,459,316 | (A)7→8 | intergenic (+5/+584) | pmbA → / ← nrdG | metalloprotease PmbA/anaerobic ribonucleoside‑triphosphate reductase activating protein |
| RA | 4,465,733 | A→G | Y150H (TAC→CAC) | treB ← | trehalose‑specific PTS enzyme IIBC component |
| RA | 4,518,648 | T→C | L41P (CTA→CCA) | insA‑7 → | KpLE2 phage‑like element; IS1 repressor protein InsA |
| RA | 4,546,393 | C→T | A433V (GCA→GTA) | fimD → | type I fimbriae usher protein |
| RA | 4,592,474 | G→A | G273E (GGG→GAG) | tsr → | methyl‑accepting chemotaxis protein Tsr |
| RA | 4,600,250 | A→G | G242G (GGT→GGC) | dnaC ← | DNA replication protein DnaC |
| RA | 4,606,094 | (G)8→9 | noncoding (72/87 nt) | leuV ← | tRNA‑Leu |
| RA | 4,624,649 | T→C | E47E (GAA→GAG) | ytjB ← | protein Smp |
| RA | 4,627,471 | C→T | R53C (CGT→TGT) | nadR → | DNA‑binding transcriptional repressor/NMN adenylyltransferase NadR |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 731797–731807 | 732217–731990 | 184–421 | 28 [19] | [23] 29 | rhsC | rhs element protein RhsC |
| * | * | ÷ | NC_000913 | 1270048–1270094 | 1270524–1270504 | 411–477 | 25 [24] | [24] 28 | ldrC–rdlC | ldrC,rdlC |
| * | * | ÷ | NC_000913 | 3423770–3424234 | 3424525–3424238 | 5–756 | 26 [20] | [22] 25 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3762345–3764072 | 3765191–3764077 | 6–2847 | 25 [24] | [23] 25 | rhsA | rhs element protein RhsA |
| * | * | ÷ | NC_000913 | 3942147–3943393 | 3946842–3946693 | 3301–4696 | 25 [23] | [23] 25 | [rrsC]–rrfC | [rrsC],gltU,rrlC,rrfC |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 21 (0.240) | 127 (1.650) | 66/242 | 0.0 | 90.2% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 9 (0.120) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 21 (0.240) | 67 (0.870) | 43/242 | 0.5 | 83.0% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 9 (0.120) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 102 (1.210) | 59/266 | 0.2 | 100% | intergenic (+253/‑33) | ychE/insH21 | putative inner membrane protein/IS5 transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 3363001 = | 109 (1.250) | 114 (1.320) | 66/272 | 0.1 | 67.6% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 1 (0.010) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 83 (0.960) | 55/274 | 0.3 | 94.3% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 5 (0.060) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||