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 | 26,664 | A→G | T130A (ACA→GCA) | ispH → | 1‑hydroxy‑2‑methyl‑2‑(E)‑butenyl 4‑diphosphate reductase |
| RA | 54,480 | T→A | I75F (ATC→TTC) | surA ← | peptidyl‑prolyl cis‑trans isomerase SurA |
| RA | 56,684 | C→T | M142I (ATG→ATA) | lptD ← | lipopolysaccharide assembly protein LptD |
| RA | 79,924 | A→G | V314A (GTT→GCT) | leuC ← | 3‑isopropylmalate dehydratase subunit LeuC |
| RA | 132,169 | A→G | A185A (GCA→GCG) | acnB → | hypothetical protein |
| RA | 167,492 | T→C | R3R (CGT→CGC) | fhuA → | ferrichrome outer membrane transporter/phage receptor |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 283,259 | A→G | H20R (CAC→CGC) | yagF → | CP4‑6 prophage; D‑xylonate dehydratase |
| RA | 285,115 | A→G | T639A (ACC→GCC) | yagF → | CP4‑6 prophage; D‑xylonate dehydratase |
| RA | 306,909 | T→C | E808E (GAA→GAG) | ecpC ← | putative fimbrial usher protein EcpC |
| RA | 318,994 | C→T | P336P (CCG→CCA) | rclA ← | putative pyridine nucleotide‑disulfide oxidoreductase RclA |
| RA | 321,746 | A→T | I47F (ATC→TTC) | ykgE → | putative lactate utilization oxidoreductase YkgE |
| RA | 335,686 | A→G | N136S (AAC→AGC) | yahD → | ankyrin repeat‑containing protein YahD |
| RA | 357,589 | G→A | intergenic (+135/+202) | codA → / ← cynR | cytosine/isoguanine deaminase/DNA‑binding transcriptional dual regulator CynR |
| RA | 520,222 | C→T | R164* (CGA→TGA) | ybbA → | putative ABC transporter ATP‑binding protein YbbA |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 589,948 | (T)5→6 | coding (1007/2973 nt) | nfrA ← | bacteriophage N4 receptor, outer membrane protein |
| RA | 769,444 | A→G | I489M (ATA→ATG) | mngB → | alpha‑mannosidase |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 916,848 | A→G | T126A (ACA→GCA) | ybjD → | DUF2813 domain‑containing protein YbjD |
| RA | 917,634 | A→G | T388A (ACG→GCG) | ybjD → | DUF2813 domain‑containing protein YbjD |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 946,407 | T→C | R179R (CGT→CGC) | ycaD → | putative transporter YcaD |
| RA | 981,608 | C→T | L188F (CTC→TTC) | ldtD → | L,D‑transpeptidase LdtD |
| RA | 985,303 | A→G | V136A (GTC→GCC) | aspC ← | aspartate aminotransferase |
| RA | 1,004,747 | A→G | intergenic (+90/‑21) | ycbF → / → pyrD | putative fimbrial chaperone YcbF/dihydroorotate dehydrogenase, type 2 |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,023,429 | A→G | V152A (GTC→GCC) | yccS ← | putative transporter YccS |
| RA | 1,031,425 | A→G | intergenic (‑7/+200) | yccA ← / ← serT | modulator of FtsH protease/tRNA‑Ser |
| RA | 1,082,810 | T→C | F190L (TTC→CTC) | efeO → | ferrous iron transport system protein EfeO |
| RA | 1,102,398 | A→G | S48S (AGT→AGC) | csgE ← | curli transport specificity factor |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,190,962 | A→G | V342A (GTG→GCG) | purB ← | adenylosuccinate lyase |
| RA | 1,214,789 | T→C | A229A (GCA→GCG) | bluF ← | blue light‑responsive regulator of BluR |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,280,679 | T→C | R272R (CGT→CGC) | narG → | nitrate reductase A subunit alpha |
| RA | 1,284,297 | (A)7→8 | coding (694/1539 nt) | narH → | nitrate reductase A subunit beta |
| RA | 1,351,398 | (C)5→6 | intergenic (‑359/+9) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase/DUF559 domain‑containing protein YcjD |
| RA | 1,363,075 | A→G | K111K (AAA→AAG) | puuC → | gamma‑glutamyl‑gamma‑aminobutyraldehyde dehydrogenase |
| RA | 1,442,442 | C→T | L134L (CTG→CTA) | ldhA ← | D‑lactate dehydrogenase |
| RA | 1,442,521 | T→C | H108R (CAC→CGC) | ldhA ← | D‑lactate dehydrogenase |
| RA | 1,470,675 | A→G | pseudogene (157/3495 nt) | ydbA → | putative outer membrane protein, N‑terminal fragment |
| RA | 1,507,895 | T→C | V372A (GTC→GCC) | rlhA → | 23S rRNA 5‑hydroxycytidine C2501 synthase |
| RA | 1,522,316 | A→G | G250G (GGT→GGC) | yncD ← | putative TonB‑dependent outer membrane receptor |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,609,008 | T→C | P5P (CCA→CCG) | yneE ← | conserved inner membrane protein YneE |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,665,903 | A→G | S197G (AGC→GGC) | clcB → | putative chloride:H(+) antiporter ClcB |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,762,529 | A→G | V494A (GTC→GCC) | sufB ← | Fe‑S cluster scaffold complex subunit SufB |
| RA | 1,840,159 | T→C | R231R (CGT→CGC) | ynjE → | molybdopterin synthase sulfurtransferase |
| RA | 1,843,243 | T→C | G291G (GGT→GGC) | gdhA → | glutamate dehydrogenase |
| RA | 1,861,665 | T→C | intergenic (‑333/+37) | ydjL ← / ← yeaC | putative zinc‑binding dehydrogenase YdjL/conserved protein YeaC |
| RA | 1,866,195 | T→C | D93G (GAC→GGC) | mipA ← | scaffolding protein that interacts with murein polymerase and murein hydrolase |
| RA | 1,872,031 | G→A | intergenic (+171/‑10) | cdgI → / → dgcJ | putative c‑di‑GMP binding protein CdgI/putative diguanylate cyclase DgcJ |
| 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 | 1,896,962 | G→A | G11R (GGG→AGG) | sdaA → | L‑serine deaminase I |
| RA | 1,926,046 | G→A | G203S (GGT→AGT) | yobB → | putative carbon‑nitrogen hydrolase family protein YobB |
| RA | 1,931,976 | (G)5→6 | coding (1096/1179 nt) | purT → | phosphoribosylglycinamide formyltransferase 2 |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,017,094 | T→C | F181L (TTT→CTT) | fliI → | flagellum‑specific ATP synthase FliI |
| RA | 2,037,637 | G→A | C172C (TGC→TGT) | hprS ← | sensory histidine kinase HprS |
| RA | 2,067,300 | C→T | G8R (GGA→AGA) | insH‑6 ← | CP4‑44 prophage; IS5 transposase and trans‑activator |
| RA | 2,075,693 | T→C | R305R (CGT→CGC) | yeeR → | CP4‑44 prophage; inner membrane protein YeeR |
| RA | 2,100,011 | T→C | T420A (ACC→GCC) | gnd ← | 6‑phosphogluconate dehydrogenase, decarboxylating |
| RA | 2,134,136 | G→A | A506V (GCG→GTG) | wzc ← | protein‑tyrosine kinase Wzc |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,287,586 | T→C | pseudogene (1329/2525 nt) | yejO ← | adhesin‑like autotransporter YejO |
| RA | 2,288,561 | (C)7→8 | pseudogene (354/2525 nt) | yejO ← | adhesin‑like autotransporter YejO |
| RA | 2,296,418 | T→C | T203A (ACC→GCC) | ccmB ← | heme trafficking system membrane protein CcmB |
| RA | 2,304,549 | C→T | intergenic (+156/+559) | eco → / ← mqo | serine protease inhibitor ecotin/malate:quinone oxidoreductase |
| RA | 2,304,561 | G→A | intergenic (+168/+547) | eco → / ← mqo | serine protease inhibitor ecotin/malate:quinone oxidoreductase |
| RA | 2,304,567 | C→T | intergenic (+174/+541) | eco → / ← mqo | serine protease inhibitor ecotin/malate:quinone oxidoreductase |
| RA | 2,363,290 | T→C | N115S (AAC→AGC) | yfaY ← | IPR008135 CinA family protein YfaY |
| RA | 2,433,257 | A→G | L224L (TTA→CTA) | accD ← | acetyl‑CoA carboxyltransferase subunit beta |
| RA | 2,440,439 | G→A | S389S (AGC→AGT) | fabB ← | beta‑ketoacyl‑[acyl carrier protein] synthase I |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,448,697 | T→C | V31A (GTC→GCC) | smrB → | putative endonuclease SmrB |
| RA | 2,513,312 | T→C | F91L (TTC→CTC) | nupC → | nucleoside:H(+) symporter NupC |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,556,707 | A→G | G197G (GGT→GGC) | eutC ← | ethanolamine ammonia‑lyase subunit beta |
| RA | 2,597,390 | T→C | T77A (ACC→GCC) | purC ← | phosphoribosylaminoimidazole‑succinocarboxamide synthase |
| RA | 2,622,640 | T→C | V136A (GTG→GCG) | purN → | phosphoribosylglycinamide formyltransferase 1 |
| RA | 2,796,713 | T→C | D25G (GAC→GGC) | kbp ← | K(+) binding protein |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,843,207 | A→G | G80G (GGT→GGC) | hycH ← | formate hydrogenlyase assembly protein |
| RA | 2,843,851 | C→T | G120G (GGG→GGA) | hycG ← | formate hydrogenlyase subunit HycG |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,943,333 | T→C | intergenic (‑188/‑4) | ygdI ← / → csdA | DUF903 domain‑containing lipoprotein YgdI/cysteine sulfinate desulfinase |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,965,981 | T→C | G19G (GGA→GGG) | lgt ← | phosphatidylglycerol‑‑prolipoprotein diacylglyceryl transferase |
| RA | 2,976,831 | T→C | V78A (GTG→GCG) | galR → | DNA‑binding transcriptional dual regulator GalR |
| RA | 2,987,060 | T→C | V405A (GTA→GCA) | yqeG → | putative transporter YqeG |
| RA | 2,990,462 | T→C | intergenic (‑102/‑92) | yqeK ← / → ygeF | protein YqeK/protein YgeF |
| RA | 3,037,451 | A→G | I219T (ATT→ACT) | recJ ← | ssDNA‑specific exonuclease RecJ |
| RA | 3,039,205 | G→A | P180L (CCG→CTG) | xerD ← | site‑specific recombinase |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,137,213 | C→T | C437Y (TGC→TAC) | gss ← | fused glutathionylspermidine amidase/glutathionylspermidine synthetase |
| RA | 3,162,019 | T→C | V217V (GTA→GTG) | ftsP ← | cell division protein required during stress conditions |
| RA | 3,170,207 | T→C | L127P (CTG→CCG) | qseB → | DNA‑binding transcriptional activator QseB |
| RA | 3,177,509 | (C)6→5 | coding (402/630 nt) | nudF ← | ADP‑sugar pyrophosphatase |
| RA | 3,188,777 | A→G | pseudogene (1346/2434 nt) | yqiG → | putative outer membrane usher protein YqiG |
| RA | 3,220,805 | T→C | C438R (TGT→CGT) | patA → | putrescine aminotransferase |
| RA | 3,236,458 | A→G | I167V (ATC→GTC) | ygjP → | putative metal‑dependent hydrolase |
| RA | 3,240,331 | C→T | R130C (CGC→TGC) | sstT → | serine/threonine:Na(+) symporter |
| RA | 3,270,481 | T→C | noncoding (112/377 nt) | rnpB ← | RNase P catalytic RNA component |
| RA | 3,299,959 | G→A | intergenic (‑44/‑7) | yhbP ← / → yhbQ | putative FMN binding protein YhbP/DNA damage response nuclease YhbQ |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,367,230 | (G)5→6 | coding (305/717 nt) | yhcF → | DUF1120 domain‑containing protein YhcF |
| RA | 3,380,178 | A→G | intergenic (‑181/‑13) | zapE ← / → yhcB | cell division factor ZapE with ATPase activity/conserved protein YhcB |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,407,268 | A→G | intergenic (+2/‑107) | accC → / → yhdT | biotin carboxylase/DUF997 domain‑containing protein YhdT |
| RA | 3,443,014 | T→C | T362A (ACG→GCG) | secY ← | Sec translocon subunit SecY |
| RA | 3,447,365 | A→G | V25A (GTC→GCC) | rplE ← | 50S ribosomal subunit protein L5 |
| RA | 3,463,948 | T→C | R9R (CGT→CGC) | gspL → | Type II secretion system protein GspL |
| RA | 3,520,382 | G→A | Q108* (CAG→TAG) | hofQ ← | DNA utilization protein HofQ |
| RA | 3,538,968 | T→C | G528G (GGT→GGC) | yhgF → | putative RNA‑binding protein YhgF |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,614,768 | T→C | F368L (TTC→CTC) | nikA → | Ni(2(+)) ABC transporter periplasmic binding protein |
| RA | 3,699,665 | A→G | A484A (GCA→GCG) | bcsG → | cellulose phosphoethanolamine transferase |
| 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 | 3,936,864 | A→G | N196S (AAC→AGC) | rbsB → | ribose ABC transporter periplasmic binding protein |
| RA | 4,124,762 | A→G | R683R (CGT→CGC) | priA ← | primosome factor N' |
| RA | 4,202,974 | T→C | I350T (ATT→ACT) | zraS → | sensory histidine kinase ZraS |
| RA | 4,237,643 | (A)7→6 | coding (10/2097 nt) | yjbH → | YjbH family protein |
| RA | 4,264,342 | A→G | Q10R (CAG→CGG) | dnaB → | replicative DNA helicase |
| RA | 4,287,902 | C→T | P47S (CCG→TCG) | nrfA → | cytochrome c552 nitrite reductase |
| RA | 4,289,528 | A→G | D95G (GAT→GGT) | nrfB → | periplasmic nitrite reductase penta‑heme c‑type cytochrome |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,307,253 | A→G | C183R (TGC→CGC) | alsK ← | D‑allose kinase |
| RA | 4,311,369 | T→C | D225G (GAC→GGC) | alsB ← | D‑allose ABC transporter periplasmic binding protein |
| RA | 4,321,059 | C→T | W63* (TGG→TGA) | phnH ← | carbon‑phosphorus lyase core complex subunit PhnH |
| RA | 4,379,256 | A→G | G37G (GGT→GGC) | frdD ← | fumarate reductase membrane protein FrdD |
| RA | 4,424,457 | (A)8→9 | intergenic (+71/+59) | ulaF → / ← yjfY | L‑ribulose‑5‑phosphate 4‑epimerase UlaF/DUF1471 domain‑containing protein YjfY |
| RA | 4,429,324 | A→G | K130K (AAA→AAG) | fklB → | FKBP‑type peptidyl‑prolyl cis‑trans isomerase FklB |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,466,074 | A→G | V36A (GTC→GCC) | treB ← | trehalose‑specific PTS enzyme IIBC component |
| RA | 4,509,793 | A→G | pseudogene (315/315 nt) | insO → | KpLE2 phage‑like element; IS911B regulator fragment |
| RA | 4,548,034 | C→T | A98V (GCC→GTC) | fimF → | type 1 fimbriae minor subunit FimF |
| RA | 4,602,599 | T→C | H87R (CAC→CGC) | yjjP ← | putative succinate exporter YjjP |
| RA | 4,632,658 | A→G | G642G (GGA→GGG) | slt → | soluble lytic murein transglycosylase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2066559–2067256 | 2067256 | 1–698 | 15 [14] | [14] 15 | insH‑6 | CP4‑44 prophage; IS5 transposase and trans‑activator |
| * | * | ÷ | NC_000913 | 3423782–3424234 | 3424522–3424238 | 5–741 | 15 [11] | [12] 16 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 4037964–4038687 | 4040512–4039392 | 706–2549 | 17 [13] | [14] 15 | [rrlA] | [rrlA] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 43 (0.650) | 31/268 | 0.9 | 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 = | 130 (1.900) | 110 (1.620) | 67/274 | 0.0 | 62.7% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 2 (0.030) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 81 (1.180) | 45/276 | 0.3 | 100% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 0 (0.000) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | 4542682 = | 39 (0.570) | 23 (0.360) | 22/258 | 1.5 | 38.5% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 37 (0.580) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 39 (0.570) | 15 (0.230) | 13/258 | 2.8 | 29.0% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 37 (0.580) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||