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 | 65,274 | G→T | G169G (GGC→GGA) | polB ← | DNA polymerase II |
| RA | 103,705 | A→G | D184G (GAC→GGC) | ftsQ → | cell division protein FtsQ |
| RA | 116,151 | G→A | H317Y (CAC→TAC) | hofB ← | T2SSE family protein |
| RA | 125,492 | A→G | T826A (ACT→GCT) | aceE → | pyruvate dehydrogenase E1 component |
| RA | 132,677 | A→G | T355A (ACC→GCC) | acnB → | hypothetical protein |
| RA | 150,649 | Δ1 bp | coding (305/1239 nt) | yadC ← | fimbrial tip‑adhesin YadC |
| RA | 205,511 | T→A | I129N (ATC→AAC) | dnaE → | DNA polymerase III subunit alpha |
| RA | 216,244 | A→G | Y254H (TAT→CAT) | yaeF ← | peptidase C92 family protein |
| RA | 223,396 | (A)5→4 | coding (564/576 nt) | gmhB → | D‑glycero‑beta‑D‑manno‑heptose‑1,7‑bisphosphate 7‑phosphatase |
| RA | 226,978 | A→G | noncoding (1220/2904 nt) | rrlH → | 23S ribosomal RNA |
| RA | 302,674 | T→C | intergenic (‑101/‑317) | paoA ← / → yagU | aldehyde dehydrogenase, Fe‑S subunit/inner membrane protein that contributes to acid resistance |
| RA | 312,227 | A→G | Y39C (TAT→TGT) | ykgL → | uncharacterized protein YkgL |
| RA | 373,971 | C→T | A35V (GCA→GTA) | mhpE → | 4‑hydroxy‑2‑oxovalerate aldolase |
| RA | 415,168 | C→T | A196T (GCC→ACC) | sbcC ← | ATP dependent, structure specific DNA nuclease ‑ SbcC subunit |
| RA | 499,419 | G→A | C185C (TGC→TGT) | aes ← | acetylesterase |
| RA | 543,881 | C→T | G56S (GGT→AGT) | allE ← | (S)‑ureidoglycine aminohydrolase |
| RA | 577,022 | C→T | intergenic (‑197/‑376) | nmpC ← / → essD | DLP12 prophage; putative outer membrane porin NmpC/DLP12 prophage; putative phage lysis protein |
| RA | 610,312 | G→A | A728V (GCG→GTG) | fepA ← | ferric enterobactin outer membrane transporter |
| RA | 642,114 | A→G | P9P (CCA→CCG) | ybdR → | putative Zn(2(+))‑dependent alcohol dehydrogenase YbdR |
| RA | 647,914 | A→G | V41A (GTC→GCC) | citX ← | apo‑citrate lyase phosphoribosyl‑dephospho‑CoA transferase |
| RA | 656,995 | C→T | L147F (CTC→TTC) | pagP → | Lipid IVA palmitoyltransferase |
| RA | 762,279 | A→G | N253S (AAC→AGC) | sucB → | dihydrolipoyltranssuccinylase |
| RA | 778,306 | T→C | G189G (GGT→GGC) | tolB → | Tol‑Pal system periplasmic protein TolB |
| RA | 792,069 | A→G | intergenic (‑14/+247) | galE ← / ← modF | UDP‑glucose 4‑epimerase/ABC family protein ModF |
| RA | 861,647 | C→T | W320* (TGG→TGA) | ybiW ← | putative pyruvate formate lyase |
| RA | 868,422 | (C)8→7 | coding (903/1872 nt) | gsiA → | glutathione ABC transporter ATP binding subunit GsiA |
| RA | 886,389 | A→G | G317G (GGT→GGC) | ybjJ ← | inner membrane protein YbjJ |
| RA | 934,749 | A→G | Q509R (CAA→CGA) | ftsK → | cell division DNA translocase FtsK |
| RA | 947,314 | T→C | V29A (GTT→GCT) | ycaM → | putative transporter YcaM |
| RA | 961,497 | A→G | A99A (GCA→GCG) | cmk → | cytidylate kinase |
| RA | 990,973 | A→G | T118A (ACC→GCC) | pepN → | aminopeptidase N |
| RA | 1,099,433 | T→C | G185G (GGT→GGC) | ycdX → | zinc‑binding phosphatase |
| RA | 1,196,735 | A→G | intergenic (+362/+132) | icd → / ← ymfD | isocitrate dehydrogenase/e14 prophage; putative SAM‑dependent methyltransferase |
| RA | 1,202,190 | A→G | intergenic (‑106/+69) | ymfJ ← / ← ymfK | e14 prophage; protein YmfJ/e14 prophage; putative repressor protein YmfK |
| RA | 1,253,902 | T→C | D684G (GAC→GGC) | ycgV ← | putative autotransporter adhesin YcgV |
| RA | 1,283,731 | A→G | N43S (AAC→AGC) | narH → | nitrate reductase A subunit beta |
| RA | 1,283,932 | A→G | N110S (AAC→AGC) | narH → | nitrate reductase A subunit beta |
| RA | 1,301,279 | T→C | V33A (GTC→GCC) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,311,398 | A→G | K104E (AAA→GAA) | tonB → | Ton complex subunit TonB |
| RA | 1,353,837 | T→C | I228V (ATT→GTT) | sapC ← | putrescine ABC exporter membrane protein SapC |
| RA | 1,396,030 | G→A | intergenic (‑108/‑46) | ynaI ← / → insH‑4 | small conductance mechanosensitive channel YnaI/IS5 transposase and trans‑activator |
| RA | 1,576,101 | G→A | R507C (CGT→TGT) | yddB ← | putative TonB‑dependent receptor |
| RA | 1,582,889 | A→G | intergenic (‑365/+37) | ydeN ← / ← ydeO | putative sulfatase/DNA‑binding transcriptional dual regulator YdeO |
| RA | 1,589,489 | A→G | G171G (GGT→GGC) | ydeT ← | fimbrial usher domain‑containing protein YdeT |
| RA | 1,624,717 | A→G | intergenic (‑220/‑56) | ydeI ← / → ydeJ | BOF family protein YdeI/conserved protein YdeJ |
| RA | 1,630,460 | +G | coding (454/1461 nt) | ydfI ← | putative oxidoreductase YdfI |
| RA | 1,658,544 | A→G | Y159C (TAC→TGC) | ynfE → | putative selenate reductase YnfE |
| RA | 1,689,482 | A→G | T303A (ACC→GCC) | manA → | mannose‑6‑phosphate isomerase |
| RA | 1,724,929 | T→C | E235G (GAG→GGG) | ydhF ← | putative oxidoreductase |
| RA | 1,727,494 | (G)6→7 | coding (836/1098 nt) | nemA → | N‑ethylmaleimide reductase |
| RA | 1,784,075 | G→A | D367N (GAT→AAT) | fadK → | short chain acyl‑CoA synthetase |
| RA | 1,790,264 | T→C | E327E (GAA→GAG) | ydiU ← | UPF0061 family protein YdiU |
| RA | 1,840,760 | G→A | D432N (GAC→AAC) | ynjE → | molybdopterin synthase sulfurtransferase |
| RA | 1,846,935 | G→A | P9L (CCG→CTG) | topB ← | DNA topoisomerase III |
| JC JC | 1,873,031 | IS1 (–) +9 bp | coding (991‑999/1491 nt) | dgcJ → | putative diguanylate cyclase DgcJ |
| RA | 1,957,350 | T→C | E261E (GAA→GAG) | torY ← | cytochrome c quinol dehydrogenase TorY |
| RA | 2,076,162 | G→A | V462I (GTC→ATC) | yeeR → | CP4‑44 prophage; inner membrane protein YeeR |
| RA | 2,111,263 | G→A | G238G (GGC→GGT) | rfbD ← | dTDP‑4‑dehydrorhamnose reductase |
| RA | 2,138,732 | T→C | H277H (CAT→CAC) | yegH → | inner membrane protein YegH |
| RA | 2,143,684 | (G)6→7 | coding (419/3318 nt) | dgcE → | putative diguanylate cyclase DgcE |
| RA | 2,181,198 | G→A | A35T (GCC→ACC) | yegV → | putative sugar kinase YegV |
| RA | 2,219,900 | G→A | S697F (TCC→TTC) | bglX ← | beta‑D‑glucoside glucohydrolase, periplasmic |
| RA | 2,249,807 | Δ1 bp | coding (91/1050 nt) | yeiH → | conserved inner membrane protein YeiH |
| RA | 2,304,858 | T→C | intergenic (+465/+250) | eco → / ← mqo | serine protease inhibitor ecotin/malate:quinone oxidoreductase |
| RA | 2,412,390 | A→G | Y69H (TAT→CAT) | yfbU ← | UPF0304 family protein YfbU |
| RA | 2,498,917 | A→G | I83V (ATT→GTT) | ypdA → | sensory histidine kinase YpdA |
| RA | 2,530,217 | T→C | intergenic (‑41/+30) | ligA ← / ← zipA | DNA ligase/cell division protein ZipA |
| RA | 2,577,541 | A→G | R279R (CGT→CGC) | maeB ← | malate dehydrogenase |
| RA | 2,633,639 | G→A | D144D (GAC→GAT) | guaB ← | inosine 5'‑monophosphate dehydrogenase |
| RA | 2,643,313 | T→C | N324S (AAC→AGC) | rlmN ← | 23S rRNA m(2)A2503 methyltransferase/tRNA m(2)A37 methyltransferase |
| RA | 2,655,680 | Δ1 bp | coding (679/1284 nt) | pepB ← | aminopeptidase B |
| RA | 2,667,444 | A→G | W135R (TGG→CGG) | hcaT ← | putative 3‑phenylpropionate transporter |
| RA | 2,698,079 | G→A | R158C (CGT→TGT) | pgpC ← | phosphatidylglycerophosphatase C |
| RA | 2,701,448 | T→C | V94V (GTA→GTG) | pdxJ ← | pyridoxine 5'‑phosphate synthase |
| RA | 2,734,543 | (C)8→7 | coding (492/732 nt) | pgeF ← | polyphenol oxidase YfiH |
| RA | 2,749,662 | C→T | R297C (CGC→TGC) | yfjD → | putative inner membrane protein |
| RA | 2,762,152 | G→A | G463G (GGC→GGT) | abpB ← | CP4‑57 prophage; putative helicase YfjK |
| RA | 2,799,026 | (A)5→6 | intergenic (‑531/‑138) | stpA ← / → alaE | DNA‑binding transcriptional repressor StpA with RNA chaperone activity/L‑alanine exporter |
| RA | 2,808,700 | A→G | pseudogene (385/1178 nt) | ygaY → | putative transporter YgaY, N‑terminal fragment |
| RA | 2,853,264 | T→C | I4T (ATC→ACC) | hypE → | hydrogenase maturation protein, carbamoyl dehydratase |
| RA | 2,859,878 | (T)6→5 | coding (119/657 nt) | pphB → | phosphoprotein phosphatase 2 |
| RA | 2,867,926 | (C)6→7 | coding (828/1140 nt) | nlpD ← | murein hydrolase activator NlpD |
| RA | 2,902,692 | G→A | G266D (GGT→GAT) | ygcE → | putative sugar kinase YgcE |
| RA | 2,926,163 | T→C | F272F (TTT→TTC) | queF → | 7‑cyano‑7‑deazaguanine reductase |
| RA | 2,984,393 | T→C | intergenic (‑269/+18) | kduI ← / ← yqeF | 5‑dehydro‑4‑deoxy‑D‑glucuronate isomerase/putative acyltransferase |
| RA | 3,152,410 | C→T | R59C (CGC→TGC) | metC → | cystathionine beta‑lyase/L‑cysteine desulfhydrase |
| RA | 3,193,391 | T→C | G176G (GGT→GGC) | yqiK → | protein YqiK |
| RA | 3,213,859 | C→T | N271N (AAC→AAT) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 3,240,984 | (G)7→6 | coding (1041/1245 nt) | sstT → | serine/threonine:Na(+) symporter |
| RA | 3,242,168 | T→C | T383A (ACG→GCG) | uxaA ← | D‑altronate dehydratase |
| RA | 3,270,488 | (C)7→9 | noncoding (105/377 nt) | rnpB ← | RNase P catalytic RNA component |
| RA | 3,366,764 | (C)5→6 | pseudogene (10/175 nt) | yhcE → | putative uncharacterized protein YhcE |
| RA | 3,397,891 | A→G | I163T (ATA→ACA) | yhdE ← | nucleoside triphosphate pyrophosphatase YhdE |
| RA | 3,500,871 | G→A | G321D (GGC→GAC) | frlA → | fructoselysine/psicoselysine transporter |
| RA | 3,504,886 | Δ1 bp | intergenic (+103/+49) | frlR → / ← yhfS | putative DNA‑binding transcriptional regulator FrlR/putative aminotransferase YhfS |
| RA | 3,584,362 | A→G | intergenic (+53/‑42) | yrhA → / → yrhD | putative uncharacterized protein YrhA/uncharacterized protein YrhD |
| RA | 3,728,118 | (C)8→9 | coding (1254/1455 nt) | xylB ← | xylulokinase |
| RA | 3,753,051 | T→C | Y350C (TAC→TGC) | yiaV ← | putative membrane fusion protein |
| RA | 3,815,808 | (A)8→9 | intergenic (‑40/+55) | pyrE ← / ← rph | orotate phosphoribosyltransferase/truncated RNase PH |
| RA | 3,864,354 | T→C | H152H (CAT→CAC) | yidP → | putative DNA‑binding transcriptional regulator YidP |
| RA | 3,879,217 | G→A | G301G (GGC→GGT) | gyrB ← | DNA gyrase subunit B |
| RA | 3,898,153 | T→C | G44G (GGT→GGC) | cbrC → | UPF0167 family colicin E2 tolerance protein CbrC |
| RA | 3,944,114 | (G)6→7 | noncoding (411/2904 nt) | rrlC → | 23S ribosomal RNA |
| RA | 3,970,876 | C→T | N248N (AAC→AAT) | wecB → | UDP‑N‑acetylglucosamine 2‑epimerase |
| RA | 3,990,669 | C→T | G33D (GGC→GAC) | hemC ← | hydroxymethylbilane synthase |
| RA | 4,230,870 | G→A | A173T (GCG→ACG) | rluF → | 23S rRNA pseudouridine(2604) and tRNA(Tyr) pseudouridine(35) synthase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,311,859 | A→G | S62P (TCT→CCT) | alsB ← | D‑allose ABC transporter periplasmic binding protein |
| RA | 4,327,222 | (A)6→7 | coding (88/2229 nt) | crfC → | clamp‑binding sister replication fork colocalization protein |
| RA | 4,343,031 | A→G | Q374R (CAG→CGG) | melA → | alpha‑galactosidase |
| RA | 4,385,752 | T→C | F17L (TTC→CTC) | yjeO → | conserved inner membrane protein YjeO |
| RA | 4,471,154 | A→G | S98S (AGT→AGC) | pyrI ← | aspartate carbamoyltransferase, PyrI subunit |
| RA | 4,511,665 | A→G | G250G (GGT→GGC) | fecD ← | ferric citrate ABC transporter membrane subunit FecD |
| RA | 4,557,419 | A→G | F291L (TTC→CTC) | hypT ← | DNA‑binding transcriptional dual regulator HypT |
| RA | 4,571,921 | (G)6→7 | intergenic (+6/‑493) | yjiS → / → yjiT | DUF1127 domain‑containing protein YjiS/putative uncharacterized protein YjiT |
| RA | 4,593,090 | T→C | A478A (GCT→GCC) | tsr → | methyl‑accepting chemotaxis protein Tsr |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 361207 | 361912 | 706 | 215 [213] | [213] 222 | lacA | lacA |
| * | * | ÷ | NC_000913 | 2856989 | 2857095 | 107 | 215 [209] | [0] 339 | [mutS] | [mutS] |
| * | * | ÷ | NC_000913 | 3423680–3424234 | 3424610–3424238 | 5–931 | 215 [209] | [213] 221 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 70046 = | 316 (0.880) | 321 (0.920) | 148/188 | 0.5 | 67.7% | coding (3/1701 nt) | araB | ribulokinase |
| ? | NC_000913 | 2857096 = | 0 (0.000) | coding (4/2562 nt) | mutS | DNA mismatch repair protein MutS | |||||
| * | ? | NC_000913 | 1207790 = | 253 (0.700) | 153 (0.510) | 104/162 | 2.9 | 43.8% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 182 (0.610) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 2514276 = | NA (NA) | 209 (0.580) | 129/194 | 2.5 | 53.3% | noncoding (4/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 3067172 = | 183 (0.510) | coding (2/897 nt) | ygfI | putative LysR‑type DNA‑binding transcriptional regulator YgfI | |||||
| * | ? | NC_000913 | = 2515616 | NA (NA) | 220 (0.630) | 126/188 | 2.3 | 52.6% | noncoding (1344/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | = 3067180 | 198 (0.570) | intergenic (‑7/+160) | ygfI/yggE | putative LysR‑type DNA‑binding transcriptional regulator YgfI/uncharacterized protein YggE | |||||