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 | 149,662 | (G)5→6 | intergenic (‑61/+53) | panB ← / ← yadC | 3‑methyl‑2‑oxobutanoate hydroxymethyltransferase/fimbrial tip‑adhesin YadC |
| RA | 155,284 | A→G | I48T (ATT→ACT) | htrE ← | putative fimbrial usher protein HtrE |
| RA | 164,230 | T→C | V709A (GTG→GCG) | hrpB → | putative ATP‑dependent RNA helicase HrpB |
| RA | 168,812 | C→T | F443F (TTC→TTT) | fhuA → | ferrichrome outer membrane transporter/phage receptor |
| RA | 191,337 | G→A | A161T (GCT→ACT) | tsf → | protein chain elongation factor EF‑Ts |
| RA | 200,900 | A→G | N140S (AAC→AGC) | skp → | periplasmic chaperone Skp |
| RA | 217,605 | C→T | V391M (GTG→ATG) | proS ← | proline‑‑tRNA ligase |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 334,048 | A→G | V129A (GTC→GCC) | yahB ← | putative LysR‑type DNA‑binding transcriptional regulator YahB |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 437,999 | C→T | R46H (CGT→CAT) | yajO ← | 1‑deoxyxylulose‑5‑phosphate synthase YajO |
| RA | 453,140 | G→A | L136F (CTT→TTT) | ampG ← | muropeptide:H(+) symporter |
| RA | 459,379 | T→C | R164R (CGT→CGC) | lon → | Lon protease |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 539,615 | A→G | I157V (ATC→GTC) | allB → | allantoinase |
| RA | 546,017 | T→C | H116R (CAC→CGC) | allD ← | ureidoglycolate dehydrogenase |
| RA | 782,930 | A→G | A282A (GCA→GCG) | nadA → | quinolinate synthase |
| RA | 830,191 | C→T | L151L (CTG→CTA) | cecR ← | DNA‑binding transcriptional dual regulator CecR |
| RA | 868,422 | (C)8→7 | coding (903/1872 nt) | gsiA → | glutathione ABC transporter ATP binding subunit GsiA |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 933,888 | A→G | E222G (GAG→GGG) | ftsK → | cell division DNA translocase FtsK |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,013,810 | T→C | G184G (GGT→GGC) | pqiB → | intermembrane transport protein PqiB |
| RA | 1,016,849 | C→T | G484D (GGC→GAC) | ycbZ ← | putative ATP‑dependent protease YcbZ |
| RA | 1,047,719 | A→G | F76S (TTC→TCC) | gfcD ← | putative lipoprotein GfcD |
| RA | 1,059,436 | (G)6→7 | coding (181/2547 nt) | torA → | trimethylamine N‑oxide reductase 1 |
| RA | 1,071,456 | A→G | S104P (TCG→CCG) | rutD ← | putative aminoacrylate hydrolase |
| RA | 1,131,290 | C→T | D91D (GAC→GAT) | flgB → | flagellar basal‑body rod protein FlgB |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,180,388 | +G | intergenic (+29/+91) | cobB → / ← ycfZ | protein‑lysine deacetylase/desuccinylase/putative inner membrane protein |
| RA | 1,185,872 | A→G | N10S (AAC→AGC) | pepT → | peptidase T |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,236,278 | (G)6→7 | coding (964/1533 nt) | ycgB ← | PF04293 family protein YcgB |
| RA | 1,252,395 | (G)5→6 | coding (1330/1920 nt) | dhaR → | DNA‑binding transcriptional dual regulator DhaR |
| RA | 1,279,520 | (T)7→6 | intergenic (+172/‑344) | narK → / → narG | nitrate:nitrite antiporter NarK/nitrate reductase A subunit alpha |
| RA | 1,283,009 | A→G | H1049R (CAC→CGC) | narG → | nitrate reductase A subunit alpha |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,358,731 | C→T | V153I (GTC→ATC) | puuP ← | putrescine:H(+) symporter PuuP |
| RA | 1,362,963 | A→G | D74G (GAC→GGC) | puuC → | gamma‑glutamyl‑gamma‑aminobutyraldehyde dehydrogenase |
| RA | 1,364,806 | A→G | D192G (GAC→GGC) | puuB → | gamma‑glutamylputrescine oxidase |
| RA | 1,374,051 | Δ1 bp | coding (830/882 nt) | ycjO → | putative ABC transporter membrane subunit YcjO |
| RA | 1,382,613 | G→A | G223S (GGC→AGC) | ompG → | outer membrane porin G |
| RA | 1,384,956 | C→T | D280D (GAC→GAT) | ycjX → | DUF463 domain‑containing protein YcjX |
| RA | 1,397,789 | T→C | A278A (GCA→GCG) | uspE ← | universal stress protein with a role cellular motility |
| RA | 1,403,596 | T→C | T324A (ACC→GCC) | abgA ← | p‑aminobenzoyl‑glutamate hydrolase subunit A |
| RA | 1,428,487 | G→A | A80A (GCC→GCT) | insH‑5 ← | Rac prophage; IS5 transposase and trans‑activator |
| RA | 1,428,499 | G→C | A76A (GCC→GCG) | insH‑5 ← | Rac prophage; IS5 transposase and trans‑activator |
| RA | 1,428,502 | A→G | G75G (GGT→GGC) | insH‑5 ← | Rac prophage; IS5 transposase and trans‑activator |
| RA | 1,428,505 | G→A | D74D (GAC→GAT) | insH‑5 ← | Rac prophage; IS5 transposase and trans‑activator |
| RA | 1,444,382 | A→G | T444T (ACA→ACG) | ydbH → | PF11739 family protein YdbH |
| RA | 1,452,765 | (T)5→4 | coding (878/2046 nt) | paaZ ← | oxepin‑CoA hydrolase/3‑oxo‑5,6‑dehydrosuberyl‑CoA semialdehyde dehydrogenase |
| RA | 1,456,917 | A→G | D163G (GAC→GGC) | paaE → | phenylacetyl‑CoA 1,2‑epoxidase, reductase subunit |
| RA | 1,500,962 | A→T | G130G (GGA→GGT) | tehA → | tellurite resistance protein |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,594,132 | (C)8→7 | pseudogene (3955/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,594,256 | (C)8→9 | pseudogene (3831/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,616,385 | T→C | V208A (GTC→GCC) | yneK → | protein YneK |
| RA | 1,665,195 | (T)7→6 | intergenic (+75/‑120) | dmsD → / → clcB | redox enzyme maturation protein DmsD/putative chloride:H(+) antiporter ClcB |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,701,635 | T→C | L227L (TTG→CTG) | malY → | negative regulator of MalT activity/cystathionine beta‑lyase |
| RA | 1,704,585 | T→C | V12A (GTT→GCT) | blr → | beta‑lactam resistance protein |
| RA | 1,767,351 | G→A | S445S (AGC→AGT) | ydiJ ← | putative FAD‑linked oxidoreductase |
| RA | 1,781,212 | A→G | N271S (AAC→AGC) | ydiR → | putative electron transfer flavoprotein subunit YdiR |
| RA | 1,873,384 | A→G | K448K (AAA→AAG) | dgcJ → | putative diguanylate cyclase DgcJ |
| RA | 1,875,961 | T→C | S97P (TCT→CCT) | nimT → | 2‑nitroimidazole exporter |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,942,267 | T→C | Q106R (CAG→CGG) | znuA ← | Zn(2(+)) ABC transporter periplasmic binding protein |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 1,996,183 | T→C | N217S (AAC→AGC) | sdiA ← | DNA‑binding transcriptional dual regulator SdiA |
| RA | 2,034,608 | T→C | pseudogene (558/1193 nt) | yedS → | putative outer membrane protein YedS, N‑terminal fragment |
| RA | 2,130,687 | T→C | G64G (GGA→GGG) | wcaD ← | putative colanic acid polymerase |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,210,473 | (C)6→7 | coding (1374/1845 nt) | yehQ → | SWIM zinc finger domains‑containing protein YehQ |
| RA | 2,247,728 | G→A | P269S (CCG→TCG) | lysP ← | lysine:H(+) symporter |
| RA | 2,260,172 | T→C | A413A (GCA→GCG) | fruA ← | fructose‑specific PTS multiphosphoryl transfer protein FruA |
| RA | 2,262,028 | A→G | V113A (GTC→GCC) | fruK ← | 1‑phosphofructokinase |
| RA | 2,379,938 | C→T | G236S (GGC→AGC) | menF ← | isochorismate synthase MenF |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,510,402 | T→C | V258A (GTG→GCG) | yfeO → | putative transport protein YfeO |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,639,288 | T→C | intergenic (‑5/+13) | yfgM ← / ← hisS | ancillary SecYEG translocon subunit/histidine‑‑tRNA ligase |
| RA | 2,660,953 | G→A | S193S (AGC→AGT) | iscS ← | cysteine desulfurase |
| RA | 2,680,442 | T→C | Q768Q (CAA→CAG) | yphG ← | DUF5107 domain‑containing protein YphG |
| RA | 2,718,354 | G→A | P59S (CCC→TCC) | yfiF ← | putative methyltransferase |
| RA | 2,764,173 | T→C | E327E (GAA→GAG) | abpA ← | CP4‑57 prophage; anti‑bacteriophage protein |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,854,315 | C→T | intergenic (+51/‑23) | hypE → / → fhlA | hydrogenase maturation protein, carbamoyl dehydratase/DNA‑binding transcriptional activator FhlA |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,860,067 | (T)5→6 | coding (308/657 nt) | pphB → | phosphoprotein phosphatase 2 |
| RA | 2,892,362 | G→A | G50D (GGC→GAC) | queD → | 6‑carboxy‑5,6,7,8‑tetrahydropterin synthase |
| RA | 2,921,641 | T→A | I154F (ATT→TTT) | gudP ← | galactarate/glucarate/glycerate transporter GudP |
| RA | 2,930,807 | T→C | L411P (CTG→CCG) | sdaB → | L‑serine deaminase II |
| RA | 2,942,289 | (C)5→6 | coding (279/918 nt) | gcvA ← | DNA‑binding transcriptional dual regulator GcvA |
| RA | 2,947,343 | (A)8→7 | intergenic (‑165/‑44) | mltA ← / → metZ | membrane‑bound lytic murein transglycosylase A/tRNA‑Met |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,975,730 | T→C | E95E (GAA→GAG) | aas ← | acyltransferase |
| RA | 2,998,969 | A→G | intergenic (‑141/+15) | ygeQ ← / ← glyU | protein YgeQ/tRNA‑Gly |
| RA | 3,008,054 | A→G | H182R (CAC→CGC) | ygeX → | 2,3‑diaminopropionate ammonia‑lyase |
| RA | 3,014,810 | G→A | P83L (CCC→CTC) | yqeC ← | uncharacterized protein YqeC |
| RA | 3,022,768 | C→T | H485Y (CAC→TAC) | xdhD → | fused putative xanthine/hypoxanthine oxidase: molybdopterin‑binding subunit and Fe‑S binding subunit |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,084,513 | T→C | N467D (AAC→GAC) | speA ← | arginine decarboxylase, biosynthetic |
| RA | 3,089,124 | Δ1 bp | coding (841/1395 nt) | galP → | galactose:H(+) symporter |
| RA | 3,092,325 | T→C | F150L (TTC→CTC) | gshB → | glutathione synthetase |
| RA | 3,131,407 | G→A | I334I (ATC→ATT) | yghQ ← | putative transport protein YghQ |
| RA | 3,169,642 | G→A | A12V (GCC→GTC) | ygiW ← | BOF family protein YgiW |
| RA | 3,229,122 | G→A | V79I (GTT→ATT) | ygjK → | glycoside hydrolase |
| RA | 3,240,984 | (G)7→8 | coding (1041/1245 nt) | sstT → | serine/threonine:Na(+) symporter |
| RA | 3,351,991 | T→C | E345E (GAA→GAG) | arcB ← | sensory histidine kinase ArcB |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,376,094 | (CG)4→3 | coding (1226‑1227/1368 nt) | dcuD → | putative transporter DcuD |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,401,547 | T→C | T596A (ACC→GCC) | csrD ← | regulator of CsrB and CsrC decay |
| RA | 3,456,803 | (C)6→7 | coding (427/1953 nt) | gspD → | Type II secretion system protein GspD |
| RA | 3,544,214 | G→A | P211S (CCG→TCG) | bioH ← | pimeloyl‑acyl carrier protein methyl ester esterase |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,587,299 | G→A | M119I (ATG→ATA) | yhhA → | DUF2756 domain‑containing protein YhhA |
| RA | 3,588,659 | A→G | R174R (CGT→CGC) | ugpC ← | sn‑glycerol 3‑phosphate ABC transporter ATP binding subunit |
| RA | 3,594,197 | G→A | P4S (CCA→TCA) | livG ← | branched chain amino acid/phenylalanine ABC transporter ATP binding subunit LivG |
| RA | 3,639,879 | (T)8→7 | intergenic (‑159/‑232) | uspB ← / → uspA | putative universal stress (ethanol tolerance) protein B/universal stress global stress response regulator |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,935,296 | C→T | T3T (ACC→ACT) | rbsC → | ribose ABC transporter membrane subunit |
| RA | 3,989,755 | A→G | V25A (GTG→GCG) | hemD ← | uroporphyrinogen‑III synthase |
| RA | 3,994,149 | C→T | H100H (CAC→CAT) | yzcX → | protein YzcX |
| RA | 4,045,233 | T→C | S345S (AGT→AGC) | yihF → | uncharacterized protein YihF |
| RA | 4,083,554 | C→T | A757T (GCC→ACC) | fdoG ← | formate dehydrogenase O subunit alpha |
| RA | 4,138,631 | A→G | G135G (GGT→GGC) | gldA ← | L‑1,2‑propanediol dehydrogenase/glycerol dehydrogenase |
| RA | 4,240,867 | A→G | V463A (GTC→GCC) | xylE ← | D‑xylose:H(+) symporter |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,298,980 | A→G | G129G (GGT→GGC) | fdhF ← | formate dehydrogenase H |
| RA | 4,302,315 | A→G | L255P (CTG→CCG) | mdtO ← | putative multidrug efflux pump subunit MdtO |
| RA | 4,321,418 | T→C | E93E (GAA→GAG) | phnG ← | carbon‑phosphorus lyase core complex subunit PhnG |
| RA | 4,353,616 | A→G | L368L (TTG→CTG) | lysU ← | lysine‑‑tRNA ligase/Ap4A synthetase/Ap3A synthetase |
| RA | 4,395,072 | G→A | G336E (GGG→GAG) | nnr → | NAD(P)HX epimerase/NAD(P)HX dehydratase |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,454,581 | A→G | intergenic (+3/+30) | yjfF → / ← fbp | galactofuranose ABC transporter putative membrane subunit YjtF/fructose‑1,6‑bisphosphatase 1 |
| RA | 4,463,218 | T→C | T498A (ACC→GCC) | treC ← | trehalose‑6‑phosphate hydrolase |
| RA | 4,484,128 | C→T | R51R (CGG→CGA) | holC ← | DNA polymerase III subunit chi |
| RA | 4,488,579 | (C)7→8 | coding (1485/1503 nt) | yjgR ← | DUF853 domain‑containing protein YjgR |
| RA | 4,505,793 | A→G | G169G (GGA→GGG) | yjhC → | KpLE2 phage‑like element; putative oxidoreductase YjhC |
| RA | 4,510,298 | A→G | intergenic (+165/+392) | yjhV → / ← fecE | KpLE2 phage‑like element; putative uncharacterized protein YjhV/ferric citrate ABC transporter ATP binding subunit |
| RA | 4,536,736 | A→G | Y287H (TAC→CAC) | nanS ← | N‑acetyl‑9‑O‑acetylneuraminate esterase |
| RA | 4,541,563 | T→C | intergenic (+4/‑474) | fimB → / → fimE | regulator for fimA/regulator for fimA |
| RA | 4,551,667 | A→G | N11S (AAC→AGC) | uxuA → | D‑mannonate dehydratase |
| RA | 4,551,918 | T→C | C95R (TGT→CGT) | uxuA → | D‑mannonate dehydratase |
| RA | 4,599,629 | A→G | intergenic (‑188/+66) | opgB ← / ← yjjA | phosphoglycerol transferase I/DUF2501 domain‑containing protein YjjA |
| RA | 4,606,215 | (G)8→9 | noncoding (72/87 nt) | leuP ← | tRNA‑Leu |
| RA | 4,606,331 | Δ1 bp | noncoding (71/87 nt) | leuQ ← | tRNA‑Leu |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 270638–271294 | 271482–271386 | 93–845 | 21 [19] | [18] 21 | insI‑1 | IS30 transposase |
| * | * | ÷ | NC_000913 | 1633756–1633923 | 1634909–1634640 | 718–1154 | 22 [20] | [20] 23 | [pinQ]–[ydfN] | [pinQ],tfaQ,[ydfN] |
| * | * | ÷ | NC_000913 | 3423748–3424234 | 3424526–3424239 | 6–779 | 21 [20] | [20] 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 = | 63 (0.760) | 46 (0.620) | 35/244 | 0.7 | 50.1% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 36 (0.490) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 63 (0.760) | 27 (0.370) | 23/244 | 1.7 | 37.1% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 36 (0.490) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 3363001 = | 145 (1.740) | 162 (1.960) | 72/274 | 0.0 | 68.9% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 2 (0.020) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 92 (1.100) | 66/276 | 0.1 | 94.8% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 5 (0.060) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||