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 | 78,395 | A→G | T259A (ACG→GCG) | setA → | sugar exporter SetA |
| RA | 149,558 | (T)8→7 | coding (44/795 nt) | panB ← | 3‑methyl‑2‑oxobutanoate hydroxymethyltransferase |
| RA | 167,157 | C→T | Q810* (CAG→TAG) | mrcB → | peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcB |
| RA | 206,064 | A→G | E313E (GAA→GAG) | dnaE → | DNA polymerase III subunit alpha |
| RA | 257,377 | A→G | Y284C (TAC→TGC) | frsA → | fermentation‑respiration switch protein |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 265,136 | A→G | V24A (GTC→GCC) | yafX ← | CP4‑6 prophage; protein YafX |
| RA | 286,570 | C→T | S392S (AGC→AGT) | yagG → | putative D‑xylonate transporter YagG |
| RA | 319,122 | T→C | T294A (ACC→GCC) | rclA ← | putative pyridine nucleotide‑disulfide oxidoreductase RclA |
| RA | 347,623 | T→C | K274R (AAG→AGG) | prpR ← | DNA‑binding transcriptional dual regulator PrpR |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 511,273 | A→G | V36A (GTG→GCG) V36A (GTG→GCG) |
copA ← copA ← |
Cu(+) exporting P‑type ATPase Cu(+) exporting P‑type ATPase |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 552,819 | C→T | Q94Q (CAG→CAA) | purE ← | N(5)‑carboxyaminoimidazole ribonucleotide mutase |
| RA | 705,972 | (T)9→8 | intergenic (+82/‑121) | nagE → / → glnS | N‑acetylglucosamine specific PTS enzyme IIABC component/glutamine‑‑tRNA ligase |
| RA | 814,191 | A→G | E222E (GAA→GAG) | uvrB → | excision nuclease subunit B |
| RA | 855,744 | T→C | M1M (ATG→GTG) † | ldtB ← | L,D‑transpeptidase YbiS |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 912,356 | C→T | V487M (GTG→ATG) | hcp ← | protein S‑nitrosylase |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 957,271 | A→G | K170K (AAA→AAG) | ycaP → | DUF421 domain‑containing protein YcaP |
| RA | 981,843 | A→G | D266G (GAC→GGC) | ldtD → | L,D‑transpeptidase LdtD |
| RA | 991,957 | C→T | P446S (CCG→TCG) | pepN → | aminopeptidase N |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,018,976 | (A)8→9 | intergenic (+39/+37) | matP → / ← ompA | macrodomain Ter protein/outer membrane porin A |
| RA | 1,026,812 | (C)6→7 | coding (204/459 nt) | mgsA ← | methylglyoxal synthase |
| RA | 1,067,883 | (T)7→8 | intergenic (‑175/‑198) | wrbA ← / → ymdF | NAD(P)H:quinone oxidoreductase/conserved protein YmdF |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,154,854 | T→C | V248A (GTG→GCG) | mltG → | endolytic murein transglycosylase |
| RA | 1,211,417 | T→C | pseudogene (5/165 nt) | icdC → | protein IcdC |
| RA | 1,212,088 | (C)8→9 | intergenic (‑85/+172) | iraM ← / ← ymgK | anti‑adaptor protein IraM, inhibitor of sigma(S) proteolysis/protein YmgK |
| RA | 1,219,997 | A→G | pseudogene (397/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,223,033 | T→C | D44G (GAC→GGC) | ymgI ← | uncharacterized protein YmgI |
| RA | 1,236,278 | (G)6→7 | coding (964/1533 nt) | ycgB ← | PF04293 family protein YcgB |
| RA | 1,245,996 | T→C | T461A (ACA→GCA) | treA ← | periplasmic trehalase |
| RA | 1,280,202 | G→A | M113I (ATG→ATA) | narG → | nitrate reductase A subunit alpha |
| RA | 1,430,008 | C→T | A320A (GCC→GCT) | stfR → | Rac prophage; putative membrane protein |
| RA | 1,439,814 | T→C | D324G (GAC→GGC) | ydbK ← | putative pyruvate‑flavodoxin oxidoreductase |
| RA | 1,491,204 | T→C | G101G (GGT→GGC) | cybB → | cytochrome b561 |
| RA | 1,529,959 | (T)7→6 | coding (38/483 nt) | ydcD → | uncharacterized protein YdcD |
| RA | 1,537,596 | T→C | T420A (ACC→GCC) | narY ← | nitrate reductase Z subunit beta |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,570,443 | A→G | L16P (CTT→CCT) | gadC ← | L‑glutamate:4‑aminobutyrate antiporter |
| JC | 1,594,256 | (C)8→11 | pseudogene (3831/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,701,758 | T→C | S268P (TCC→CCC) | malY → | negative regulator of MalT activity/cystathionine beta‑lyase |
| RA | 1,727,494 | (G)6→7 | coding (836/1098 nt) | nemA → | N‑ethylmaleimide reductase |
| RA | 1,765,480 | C→T | G51G (GGG→GGA) | menI ← | 1,4‑dihydroxy‑2‑naphthoyl‑CoA hydrolase |
| RA | 1,873,384 | A→G | K448K (AAA→AAG) | dgcJ → | putative diguanylate cyclase DgcJ |
| RA | 1,879,732 | G→A | Q73* (CAG→TAG) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,908,699 | A→G | V23A (GTA→GCA) | mgrB ← | PhoQ kinase inhibitor |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,010,684 | T→C | S29P (TCT→CCT) | yedL → | putative acetyltransferase YedL |
| RA | 2,046,679 | T→G | I581S (ATC→AGC) | yeeJ → | inverse autotransporter adhesin |
| RA | 2,135,135 | (C)5→6 | coding (518/2163 nt) | wzc ← | protein‑tyrosine kinase Wzc |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,286,652 | T→C | pseudogene (2263/2525 nt) | yejO ← | adhesin‑like autotransporter YejO |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,492,467 | T→G | D263A (GAT→GCT) | frc ← | formyl‑CoA transferase |
| RA | 2,512,088 | T→C | T207A (ACG→GCG) | mntH ← | Mn(2(+))/Fe(2(+)): H(+) symporter MntH |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,540,397 | C→T | G140S (GGC→AGC) | cysA ← | sulfate/thiosulfate ABC transporter ATP binding subunit |
| RA | 2,553,284 | T→C | C20C (TGT→TGC) | hemF → | coproporphyrinogen III oxidase |
| RA | 2,560,085 | (T)6→7 | intergenic (+19/‑172) | intZ → / → yffL | CPZ‑55 prophage; putative phage integrase IntZ/CPZ‑55 prophage; uncharacterized protein YffL |
| RA | 2,610,540 | +C | coding (377/546 nt) | hyfH → | hydrogenase 4 component H |
| RA | 2,696,623 | G→A | V275I (GTC→ATC) | mltF → | membrane‑bound lytic murein transglycosylase F |
| RA | 2,719,182 | T→C | intergenic (+28/‑41) | trxC → / → yfiP | reduced thioredoxin 2/conserved protein YfiP |
| RA | 2,741,044 | T→C | Q36R (CAG→CGG) | aroF ← | 3‑deoxy‑7‑phosphoheptulonate synthase, Tyr‑sensitive |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,911,527 | T→C | T709A (ACC→GCC) | relA ← | GDP/GTP pyrophosphokinase |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,969,880 | T→C | A73A (GCT→GCC) | mutH → | DNA mismatch repair protein MutH |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,075,094 | T→C | I34M (ATA→ATG) | fumE ← | fumarase E |
| RA | 3,090,827 | G→A | A161T (GCT→ACT) | endA → | DNA‑specific endonuclease I |
| RA | 3,097,496 | T→C | M77T (ATG→ACG) | yggW → | putative coproporphyrinogen‑III oxidase‑like protein YggW |
| RA | 3,193,857 | A→G | T332A (ACG→GCG) | yqiK → | protein YqiK |
| RA | 3,210,329 | T→C | D72G (GAC→GGC) | tsaD ← | N(6)‑L‑threonylcarbamoyladenine synthase, TsaD subunit |
| RA | 3,220,362 | A→G | N290S (AAC→AGC) | patA → | putrescine aminotransferase |
| RA | 3,237,548 | A→G | T80A (ACA→GCA) | ygjR → | putative oxidoreductase YgjR |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,374,227 | T→C | N88S (AAC→AGC) | nanR ← | DNA‑binding transcriptional dual regulator NanR |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,432,403 | A→G | V21A (GTG→GCG) | smg ← | DUF494 domain‑containing protein Smg |
| RA | 3,517,815 | T→C | E224E (GAA→GAG) | aroB ← | 3‑dehydroquinate synthase |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,564,129 | T→C | intergenic (‑124/+5) | yzgL ← / ← glgP | putative uncharacterized protein YzgL/glycogen phosphorylase |
| RA | 3,607,133 | T→C | V228A (GTT→GCT) | zntA → | Zn(2(+))/Cd(2(+))/Pb(2(+)) exporting P‑type ATPase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,822,373 | C→T | R90C (CGT→TGT) | rpoZ → | RNA polymerase subunit omega |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,860,661 | C→A | Q127K (CAA→AAA) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,865,102 | A→G | V391A (GTG→GCG) | yidE ← | putative transport protein YidE |
| RA | 3,930,634 | A→G | S154P (TCC→CCC) | ravA ← | regulatory ATPase RavA |
| RA | 3,946,348 | (G)6→7 | noncoding (2645/2904 nt) | rrlC → | 23S ribosomal RNA |
| RA | 3,989,527 | T→C | Q101R (CAG→CGG) | hemD ← | uroporphyrinogen‑III synthase |
| RA | 4,074,920 | (A)8→7 | coding (252/786 nt) | yihW → | putative DNA‑binding transcriptional regulator YihW |
| RA | 4,101,728 | (G)7→8 | coding (39/984 nt) | kdgT → | 2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| RA | 4,114,186 | C→T | G96E (GGA→GAA) | fpr ← | flavodoxin/ferredoxin‑NADP(+) reductase |
| RA | 4,196,057 | C→T | A15T (GCC→ACC) | thiC ← | phosphomethylpyrimidine synthase |
| RA | 4,217,787 | A→G | T227A (ACC→GCC) | aceA → | isocitrate lyase |
| RA | 4,295,048 | C→T | R190C (CGC→TGC) | gltP → | glutamate/aspartate : H(+) symporter GltP |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,373,642 | A→G | V198A (GTG→GCG) | yjeJ ← | protein YjeJ |
| RA | 4,383,874 | A→G | G12G (GGA→GGG) | yjeM → | putative transporter YjeM |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,509,233 | A→G | pseudogene (225/471 nt) | insO → | KpLE2 phage‑like element; IS911B regulator fragment |
| RA | 4,523,001 | A→G | V365A (GTG→GCG) | yjhG ← | KpLE2 phage‑like element; D‑xylonate dehydratase |
| RA | 4,535,720 | A→G | pseudogene (706/1017 nt) | yjhR → | KpLE2 phage‑like element; PLD‑like domain‑containing protein YjhR |
| RA | 4,561,864 | (C)6→7 | coding (812/1179 nt) | yjiJ ← | putative transporter YjiJ |
| RA | 4,565,901 | A→G | intergenic (‑51/+65) | yjiM ← / ← yjiN | putative dehydratase subunit/DUF445 domain‑containing protein YjiN |
| RA | 4,610,011 | A→G | T200A (ACC→GCC) | prfC → | peptide chain release factor RF3 |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1427841–1427892 | 1428629–1428588 | 697–789 | 32 [24] | [31] 32 | insH‑5 | Rac prophage; IS5 transposase and trans‑activator |
| * | * | ÷ | NC_000913 | 1640915 | 1641074 | 160 | 32 [31] | [30] 32 | essQ/cspB | Qin prophage; putative S lysis protein/Qin prophage; cold shock‑like protein CspB |
| * | * | ÷ | NC_000913 | 2033767 | 2033973 | 207 | 32 [31] | [27] 37 | rseX/yedS | small regulatory RNA RseX/putative outer membrane protein YedS, N‑terminal fragment |
| * | * | ÷ | NC_000913 | 3423770–3424234 | 3424525–3424238 | 5–756 | 39 [28] | [23] 33 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3455399 | 3455626 | 228 | 33 [31] | [31] 35 | [gspC] | [gspC] |
| * | * | ÷ | NC_000913 | 3751906 | 3752009 | 104 | 36 [28] | [31] 33 | [yiaU] | [yiaU] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 67 (0.690) | 44 (0.510) | 30/246 | 1.5 | 43.3% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 56 (0.650) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 67 (0.690) | 30 (0.350) | 29/246 | 1.6 | 34.2% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 56 (0.650) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 62 (0.650) | 37/270 | 1.2 | 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 = | 136 (1.390) | 150 (1.550) | 63/276 | 0.2 | 68.8% | 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) | 127 (1.300) | 63/278 | 0.2 | 93.4% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 9 (0.090) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||