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 | 91,043 | A→G | R4R (AGA→AGG) | ftsL → | cell division protein FtsL |
| RA | 92,589 | T→C | L393L (TTG→CTG) | ftsI → | peptidoglycan DD‑transpeptidase FtsI |
| RA | 118,297 | C→T | G117S (GGC→AGC) | nadC ← | quinolinate phosphoribosyltransferase (decarboxylating) |
| RA | 133,532 | A→G | T640A (ACC→GCC) | acnB → | hypothetical protein |
| RA | 144,925 | G→A | V117I (GTC→ATC) | yadI → | putative PTS enzyme IIA component YadI |
| RA | 193,408 | A→G | E179E (GAA→GAG) | frr → | ribosome‑recycling factor |
| RA | 217,026 | (A)7→8 | intergenic (‑23/+31) | yaeF ← / ← proS | peptidase C92 family protein/proline‑‑tRNA ligase |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 262,808 | C→T | intergenic (+52/‑63) | proA → / → thrW | glutamate‑5‑semialdehyde dehydrogenase/tRNA‑Thr |
| RA | 263,031 | T→C | intergenic (+85/+119) | thrW → / ← ykfN | tRNA‑Thr/YdiA family protein |
| RA | 352,394 | G→A | D394N (GAC→AAC) | prpD → | 2‑methylcitrate dehydratase |
| RA | 359,656 | C→T | D56D (GAC→GAT) | cynS → | cyanase |
| RA | 360,769 | C→T | R260W (CGG→TGG) | cynX → | cyanate transporter |
| RA | 380,022 | (G)10→11 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 413,751 | G→A | A668V (GCG→GTG) | sbcC ← | ATP dependent, structure specific DNA nuclease ‑ SbcC subunit |
| RA | 430,579 | C→T | intergenic (+103/‑26) | secF → / → yajD | Sec translocon accessory complex subunit SecF/HNH nuclease family protein |
| RA | 448,630 | C→T | A11T (GCC→ACC) | cyoC ← | cytochrome bo3 ubiquinol oxidase subunit 3 |
| RA | 464,281 | A→G | E115E (GAA→GAG) | ybaV → | helix‑hairpin‑helix 3 family protein |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 549,638 | C→T | I4I (ATC→ATT) | ylbF → | DUF2877 domain‑containing protein YlbF |
| RA | 632,017 | (G)7→8 | intergenic (+18/‑165) | cstA → / → ybdD | carbon starvation protein A/conserved protein YbdD |
| RA | 634,857 | C→T | G174S (GGC→AGC) | ybdM ← | ParB‑like nuclease domain‑containing protein YbdM |
| RA | 733,366 | A→G | T1262A (ACT→GCT) | rhsC → | rhs element protein RhsC |
| RA | 766,957 | (G)6→7 | coding (974/1977 nt) | mngA → | 2‑O‑alpha‑mannosyl‑D‑glycerate specific PTS enzyme II |
| RA | 826,783 | T→C | N157S (AAC→AGC) | ybhS ← | putative ABC exporter membrane subunit YbhS |
| RA | 880,066 | C→T | A139T (GCC→ACC) | gstB ← | glutathione S‑transferase GstB |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 952,422 | T→C | E378G (GAA→GGA) | pflB ← | pyruvate formate‑lyase |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,046,072 | A→G | V625A (GTA→GCA) | gfcD ← | putative lipoprotein GfcD |
| RA | 1,090,516 | C→T | E592K (GAG→AAG) | pgaA ← | partially deacetylated poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine outer membrane porin |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,157,814 | (C)6→7 | intergenic (+240/‑55) | ycfH → / → ptsG | putative metal‑dependent hydrolase YcfH/glucose‑specific PTS enzyme IIBC component |
| RA | 1,185,300 | C→T | A99T (GCA→ACA) | potA ← | spermidine preferential ABC transporter ATP binding subunit |
| RA | 1,212,088 | (C)8→7 | intergenic (‑85/+172) | iraM ← / ← ymgK | anti‑adaptor protein IraM, inhibitor of sigma(S) proteolysis/protein YmgK |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,222,450 | A→G | V62A (GTT→GCT) | ymgD ← | PF16456 family protein YmgD |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,346,417 | C→T | G109E (GGG→GAG) | pdeR ← | cyclic di‑GMP phosphodiesterase PdeR |
| RA | 1,398,576 | T→C | D16G (GAC→GGC) | uspE ← | universal stress protein with a role cellular motility |
| RA | 1,399,978 | T→C | T87A (ACG→GCG) | ogt ← | methylated‑DNA‑‑[protein]‑cysteine S‑methyltransferase |
| RA | 1,410,385 | C→T | A292V (GCC→GTC) | dbpA → | ATP‑dependent RNA helicase DbpA |
| RA | 1,420,807 | +C | coding (124/423 nt) | ydaT → | Rac prophage; protein YdaT |
| RA | 1,431,622 | C→T | V858V (GTC→GTT) | stfR → | Rac prophage; putative membrane protein |
| RA | 1,460,265 | G→A | A404A (GCG→GCA) | paaH → | 3‑hydroxyadipyl‑CoA dehydrogenase |
| RA | 1,492,246 | A→G | intergenic (+72/‑224) | sokB → / → trg | putative small regulatory RNA SokB/methyl‑accepting chemotaxis protein Trg |
| RA | 1,529,541 | T→C | pseudogene (1652/2049 nt) | rhsE → | RhsE protein in rhs element |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,594,132 | (C)8→9 | pseudogene (3955/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,632,654 | T→C | intergenic (‑369/‑236) | ydfJ ← / → ynfT | putative transporter YdfJ/Qin prophage; protein YnfT |
| RA | 1,666,153 | A→G | N280S (AAC→AGC) | clcB → | putative chloride:H(+) antiporter ClcB |
| RA | 1,669,062 | G→A | P177P (CCC→CCT) | ynfL ← | putative DNA‑binding transcriptional regulator |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,700,710 | T→C | V452V (GTT→GTC) | malX → | PTS enzyme IIBC component MalX |
| RA | 1,727,494 | (G)6→7 | coding (836/1098 nt) | nemA → | N‑ethylmaleimide reductase |
| RA | 1,752,659 | T→C | Y391C (TAC→TGC) | ydhV ← | putative oxidoreductase |
| RA | 1,786,989 | C→T | G42S (GGT→AGT) | ppsA ← | phosphoenolpyruvate synthetase |
| RA | 1,812,917 | T→C | G72G (GGA→GGG) | ydjO ← | protein YdjO |
| RA | 1,821,867 | (A)8→9 | intergenic (‑248/+51) | chbB ← / ← osmE | N,N'‑diacetylchitobiose‑specific PTS enzyme IIB component/osmotically‑inducible lipoprotein OsmE |
| RA | 1,867,413 | G→A | R169H (CGC→CAC) | yeaG → | protein kinase YeaG |
| 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 |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,012,563 | (G)6→7 | pseudogene (62/279 nt) | intG → | putative defective phage integrase |
| RA | 2,067,300 | C→T | G8R (GGA→AGA) | insH‑6 ← | CP4‑44 prophage; IS5 transposase and trans‑activator |
| RA | 2,109,879 | T→C | D87G (GAT→GGT) | rfbC ← | dTDP‑4‑dehydrorhamnose 3,5‑epimerase |
| RA | 2,118,073 | A→G | F111S (TTC→TCC) | wcaK ← | putative colanic acid biosynthesis pyruvyl transferase |
| RA | 2,150,824 | T→C | K54K (AAA→AAG) | yegI ← | protein kinase YegI |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,185,875 | (G)7→8 | intergenic (‑79/‑42) | rcnR ← / → rcnA | DNA‑binding transcriptional repressor RcnR/Ni(2(+))/Co(2(+)) exporter |
| RA | 2,265,666 | G→A | D73N (GAC→AAC) | yeiP → | elongation factor P family protein |
| RA | 2,273,984 | C→T | R541* (CGA→TGA) | yejA → | putative oligopeptide ABC transporter periplasmic binding protein |
| RA | 2,288,561 | (C)7→8 | pseudogene (354/2525 nt) | yejO ← | adhesin‑like autotransporter YejO |
| RA | 2,300,312 | T→C | K814K (AAA→AAG) | napA ← | periplasmic nitrate reductase subunit NapA |
| RA | 2,321,258 | G→A | A406T (GCT→ACT) | atoS → | sensory histidine kinase AtoS |
| RA | 2,339,161 | T→C | D87G (GAC→GGC) | gyrA ← | DNA gyrase subunit A |
| RA | 2,388,965 | G→A | D111N (GAT→AAT) | yfbO → | uncharacterized protein YfbO |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,453,124 | A→G | pseudogene (1878/2646 nt) | yfcU ← | putative outer membrane usher protein YfcU |
| RA | 2,457,339 | T→C | T607T (ACA→ACG) | fadJ ← | 3‑hydroxyacyl‑CoA dehydrogenase FadJ |
| RA | 2,482,013 | C→T | G55D (GGC→GAC) | emrY ← | tripartite efflux pump membrane subunit EmrY |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,541,004 | C→T | G226S (GGC→AGC) | cysW ← | sulfate/thiosulfate ABC transporter inner membrane subunit CysW |
| RA | 2,564,978 | G→A | A152A (GCG→GCA) | yffS → | CPZ‑55 prophage; uncharacterized protein YffS |
| RA | 2,601,501 | G→A | G101R (GGA→AGA) | hyfA → | hydrogenase 4 component A |
| RA | 2,658,666 | T→C | G90G (GGA→GGG) | hscA ← | iron‑sulfur cluster biosynthesis chaperone HscA |
| RA | 2,667,412 | C→T | A145A (GCG→GCA) | hcaT ← | putative 3‑phenylpropionate transporter |
| RA | 2,716,589 | T→C | intergenic (‑140/‑165) | grcA ← / → ung | stress‑induced alternate pyruvate formate‑lyase subunit/uracil‑DNA glycosylase |
| RA | 2,722,300 | C→T | A783V (GCG→GTG) | patZ → | peptidyl‑lysine acetyltransferase |
| RA | 2,725,159 | T→C | G196G (GGA→GGG) | kgtP ← | alpha‑ketoglutarate:H(+) symporter |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,818,331 | G→T | intergenic (‑57/+142) | argY ← / ← argV | tRNA‑Arg/tRNA‑Arg |
| RA | 2,824,303 | T→C | Q15R (CAG→CGG) | pncC ← | NMN aminohydrolase |
| RA | 2,853,629 | G→A | A126T (GCC→ACC) | hypE → | hydrogenase maturation protein, carbamoyl dehydratase |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,883,098 | (C)6→7 | coding (1041/1509 nt) | casA ← | type I‑E CRISPR system Cascade subunit CasA |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,955,096 | T→C | E303G (GAA→GGA) | recB ← | exodeoxyribonuclease V subunit RecB |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,102,340 | (C)6→7 | coding (513/720 nt) | trmI ← | tRNA m(7)G46 methyltransferase |
| RA | 3,117,500 | T→C | N538S (AAC→AGC) | yghJ ← | putative lipoprotein YghJ |
| RA | 3,166,231 | C→T | P496P (CCG→CCA) | ygiS ← | putative deoxycholate binding periplasmic protein |
| RA | 3,169,857 | G→A | M10I (ATG→ATA) | qseB → | DNA‑binding transcriptional activator QseB |
| RA | 3,170,984 | G→A | W167* (TGG→TGA) | qseC → | sensory histidine kinase QseC |
| RA | 3,175,678 | T→C | Y110C (TAC→TGC) | yqiA ← | esterase YqiA |
| RA | 3,177,351 | T→C | N187S (AAC→AGC) | nudF ← | ADP‑sugar pyrophosphatase |
| RA | 3,178,848 | T→C | L245P (CTG→CCG) | tolC → | outer membrane channel TolC |
| RA | 3,188,180 | T→C | pseudogene (749/2434 nt) | yqiG → | putative outer membrane usher protein YqiG |
| RA | 3,240,984 | (G)7→8 | coding (1041/1245 nt) | sstT → | serine/threonine:Na(+) symporter |
| RA | 3,277,706 | (A)7→8 | coding (370/465 nt) | yhaV → | ribosome‑dependent mRNA interferase toxin YhaV |
| RA | 3,307,964 | T→C | intergenic (‑31/+76) | yrbN ← / ← nlpI | uncharacterized protein YrbN/lipoprotein NlpI |
| RA | 3,315,652 | T→C | E121E (GAA→GAG) | infB ← | translation initiation factor IF‑2 |
| RA | 3,344,150 | G→A | L69L (CTG→CTA) | lptB → | lipopolysaccharide transport system ATP binding protein |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,362,541 | T→C | F144L (TTC→CTC) | yhcA → | putative fimbrial chaperone YhcA |
| RA | 3,377,428 | T→C | intergenic (‑8/+387) | sspA ← / ← rpsI | stringent starvation protein A/30S ribosomal subunit protein S9 |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,407,691 | A→G | T29A (ACC→GCC) | panF → | pantothenate:Na(+) symporter |
| RA | 3,414,561 | A→G | N233S (AAT→AGT) | acrE → | multidrug efflux pump membrane fusion lipoprotein AcrE |
| RA | 3,415,885 | C→T | P285S (CCG→TCG) | acrF → | multidrug efflux pump RND permease AcrF |
| RA | 3,432,266 | G→A | P67S (CCT→TCT) | smg ← | DUF494 domain‑containing protein Smg |
| RA | 3,473,215 | T→C | E100E (GAA→GAG) | fusA ← | elongation factor G |
| RA | 3,487,815 | A→G | D342G (GAC→GGC) | yhfK → | putative transporter YhfK |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,643,053 | T→C | H27R (CAC→CGC) | rsmJ ← | 16S rRNA m(2)G1516 methyltransferase |
| RA | 3,657,230 | T→C | V79A (GTA→GCA) | hdeD → | acid‑resistance membrane protein |
| RA | 3,685,370 | G→A | S83S (AGC→AGT) | pdeK ← | putative c‑di‑GMP phosphodiesterase PdeK |
| RA | 3,789,118 | G→A | R322C (CGC→TGC) | waaH ← | UDP‑glucuronate:LPS(HepIII) glycosyltransferase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,844,578 | A→G | A205A (GCA→GCG) | adeD → | adenine deaminase |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,920,044 | T→C | Q120Q (CAA→CAG) | atpH ← | ATP synthase F1 complex subunit delta |
| RA | 3,923,928 | A→G | L569P (CTG→CCG) | mnmG ← | 5‑carboxymethylaminomethyluridine‑tRNA synthase subunit MnmG |
| RA | 3,942,117 | G→A | noncoding (310/1542 nt) | rrsC → | 16S ribosomal RNA |
| RA | 3,951,513 | A→G | pseudogene (954/1645 nt) | ilvG → | acetolactate synthase II subunit IlvG, N‑terminal fragment (pseudogene) |
| RA | 3,965,207 | T→C | T142A (ACG→GCG) | rhlB ← | ATP‑dependent RNA helicase RhlB |
| RA | 3,976,801 | C→T | A175V (GCG→GTG) | wzxE → | lipid III flippase |
| RA | 4,081,038 | T→C | Q64R (CAG→CGG) | fdhE ← | formate dehydrogenase formation protein |
| RA | 4,091,007 | C→T | A454T (GCG→ACG) | frvB ← | putative PTS enzyme IIBC component FrvB |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,345,152 | A→G | V136A (GTC→GCC) | yjdF ← | conserved inner membrane protein YjdF |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,491,746 | A→G | G260G (GGT→GGC) | idnT ← | L‑idonate/5‑ketogluconate/gluconate transporter |
| RA | 4,606,330 | (G)8→9 | noncoding (72/87 nt) | leuQ ← | tRNA‑Leu |
| RA | 4,624,114 | A→G | S2P (TCC→CCC) | lplA ← | lipoate‑‑protein ligase A |
| RA | 4,632,782 | C→T | S8L (TCA→TTA) | trpR → | DNA‑binding transcriptional repressor TrpR |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1633297–1633613 | 1633946–1633925 | 313–650 | 22 [21] | [21] 22 | [ydfK]–[pinQ] | [ydfK],[pinQ] |
| * | * | ÷ | NC_000913 | 1634181–1634637 | 1634911–1634642 | 6–731 | 22 [21] | [19] 24 | [pinQ]–[ydfN] | [pinQ],tfaQ,[ydfN] |
| * | * | ÷ | NC_000913 | 2066554–2067264 | 2067264 | 1–711 | 23 [19] | [19] 22 | insH‑6 | CP4‑44 prophage; IS5 transposase and trans‑activator |
| * | * | ÷ | NC_000913 | 2817983 | 2818324 | 342 | 22 [20] | [18] 27 | argZ–argY | argZ,argY |
| * | * | ÷ | NC_000913 | 3423767–3424234 | 3424531–3424238 | 5–765 | 22 [21] | [21] 22 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 47 (0.630) | 43 (0.650) | 30/244 | 0.9 | 49.8% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 45 (0.680) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 47 (0.630) | 27 (0.410) | 21/244 | 1.8 | 38.4% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 45 (0.680) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 3363001 = | 109 (1.450) | 122 (1.640) | 55/274 | 0.1 | 69.1% | 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) | 93 (1.240) | 58/276 | 0.1 | 93.9% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 6 (0.080) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||