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 | 34,120 | (T)9→8 | intergenic (+82/‑180) | carB → / → caiF | carbamoyl phosphate synthetase subunit beta/DNA‑binding transcriptional activator CaiF |
| RA | 42,958 | T→C | S186P (TCC→CCC) | fixA → | putative electron transfer flavoprotein FixA |
| RA | 69,037 | A→G | F338L (TTT→CTT) | araB ← | ribulokinase |
| RA | 137,719 | A→G | T213A (ACG→GCG) | cueO → | cuprous oxidase/multicopper oxidase with role in copper homeostasis |
| RA | 145,411 | A→G | T111A (ACG→GCG) | yadE → | putative polysaccharide deacetylase lipoprotein |
| RA | 147,117 | T→C | S50S (AGT→AGC) | rpnC → | recombination‑promoting nuclease RpnC |
| RA | 230,227 | A→G | S219P (TCA→CCA) | yafC ← | putative LysR family transcriptional regulator YafC |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 294,481 | G→A | R107* (CGA→TGA) | yagM ← | CP4‑6 prophage; protein YagM |
| RA | 301,033 | C→T | T285T (ACG→ACA) | paoB ← | aldehyde dehydrogenase, FAD‑binding subunit |
| RA | 339,723 | T→C | C467R (TGC→CGC) | yahG → | DUF1116 domain‑containing protein YahG |
| RA | 363,067 | T→C | N38S (AAC→AGC) | lacY ← | lactose permease |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 401,384 | A→G | intergenic (‑461/‑2) | ddlA ← / → iraP | D‑alanine‑‑D‑alanine ligase A/anti‑adaptor protein for sigma(S) stabilization |
| RA | 443,547 | A→G | V32A (GTC→GCC) | yajL ← | protein/nucleic acid deglycase 3 |
| RA | 445,303 | (T)6→5 | coding (1364/1365 nt) | yajR ← | putative major facilitator superfamily transport protein YajR |
| RA | 490,996 | T→C | F39L (TTT→CTT) | ybaN → | conserved inner membrane protein YbaN |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 589,167 | T→C | E596E (GAA→GAG) | nfrA ← | bacteriophage N4 receptor, outer membrane protein |
| RA | 779,742 | T→C | S49P (TCT→CCT) | cpoB → | cell division coordinator CpoB |
| RA | 842,301 | T→C | intergenic (‑245/‑31) | mcbA ← / → rlmF | DUF1471 domain‑containing protein McbA/23S rRNA m(6)A1618 methyltransferase |
| RA | 872,925 | A→G | intergenic (+124/‑54) | gsiD → / → pdeI | glutathione ABC transporter membrane subunit GsiD/putative c‑di‑GMP phosphodiesterase PdeI |
| 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 | 995,967 | (A)5→4 | coding (22/1146 nt) | ssuD ← | FMNH2‑dependent alkanesulfonate monooxygenase |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,028,126 | T→C | Y61H (TAT→CAT) | yccU → | putative CoA‑binding protein with NAD(P)‑binding Rossmann‑fold domain |
| RA | 1,034,314 | A→G | Y354C (TAT→TGT) | hyaB → | hydrogenase 1 large subunit |
| RA | 1,101,354 | T→C | I111V (ATT→GTT) | csgG ← | curli secretion channel |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,182,601 | A→G | Y77H (TAT→CAT) | potD ← | spermidine preferential ABC transporter periplasmic binding protein |
| RA | 1,188,199 | T→C | E14E (GAA→GAG) | roxA ← | ribosomal protein‑arginine oxygenase |
| RA | 1,205,073 | G→A | V302M (GTG→ATG) pseudogene (673/1137 nt) |
ymfN → aaaE → |
e14 prophage; chimeric replication protein/phage terminase YmfN phage terminase |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,240,911 | A→G | A387A (GCT→GCC) | cvrA ← | putative K(+):H(+) antiporter |
| RA | 1,271,390 | C→T | V154I (GTA→ATA) | chaA ← | Na(+)/K(+):H(+) antiporter ChaA |
| RA | 1,271,406 | (G)5→6 | coding (444/1101 nt) | chaA ← | Na(+)/K(+):H(+) antiporter ChaA |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,377,427 | G→A | G199D (GGC→GAC) | ycjS → | putative oxidoreductase YcjS |
| RA | 1,399,985 | (C)7→8 | coding (252/516 nt) | ogt ← | methylated‑DNA‑‑[protein]‑cysteine S‑methyltransferase |
| RA | 1,432,013 | A→G | K989E (AAA→GAA) | stfR → | Rac prophage; putative membrane protein |
| RA | 1,481,669 | A→G | Y254C (TAC→TGC) | ynbD → | putative phosphatase |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,564,818 | A→G | S306P (TCA→CCA) | dosP ← | oxygen‑sensing c‑di‑GMP phosphodiesterase DosP |
| RA | 1,594,132 | (C)8→9 | pseudogene (3955/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,635,023 | T→C | A275A (GCA→GCG) | ydfN ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,635,026 | A→G | H274H (CAT→CAC) | ydfN ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,635,029 | C→T | A273A (GCG→GCA) | ydfN ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,635,032 | G→A | G272G (GGC→GGT) | ydfN ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,635,059 | C→T | S263S (TCG→TCA) | ydfN ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,657,835 | T→C | S91P (TCT→CCT) | ynfD → | DUF1161 domain‑containing protein YnfD |
| RA | 1,667,961 | C→T | A202T (GCA→ACA) | mlc ← | DNA‑binding transcriptional repressor Mlc |
| RA | 1,679,855 | T→C | V100A (GTC→GCC) | ydgI → | putative arginine:ornithine antiporter |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,761,775 | T→C | N6S (AAC→AGC) E246E (GAA→GAG) |
sufD ← sufC ← |
Fe‑S cluster scaffold complex subunit SufD Fe‑S cluster scaffold complex subunit SufC |
| RA | 1,769,478 | (G)7→8 | coding (405/1113 nt) | ydiK → | putative transporter YdiK |
| RA | 1,802,766 | T→C | intergenic (‑196/‑328) | thrS ← / → arpB | threonine‑‑tRNA ligase/putative ankyrin repeat protein B, N‑terminal fragment |
| RA | 1,818,550 | (C)7→6 | intergenic (‑50/+55) | chbF ← / ← chbR | monoacetylchitobiose‑6‑phosphate hydrolase/DNA‑binding transcriptional dual regulator ChbR |
| RA | 1,857,011 | T→C | E253E (GAA→GAG) | ydjI ← | putative aldolase YdjI |
| 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 | 1,884,146 | T→C | V320A (GTA→GCA) | yeaV → | putative transporter YeaV |
| RA | 1,946,417 | T→C | V56A (GTT→GCT) | yebB → | putative papain‑like amidase YebB |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 1,984,599 | C→T | A157A (GCG→GCA) | araG ← | arabinose ABC transporter ATP binding subunit |
| RA | 1,991,910 | A→G | intergenic (‑9/+4) | leuZ ← / ← cysT | tRNA‑Leu/tRNA‑Cys |
| RA | 2,017,557 | A→G | Q335R (CAG→CGG) | fliI → | flagellum‑specific ATP synthase FliI |
| RA | 2,031,989 | C→T | C110Y (TGC→TAC) | dcm ← | DNA‑cytosine methyltransferase |
| RA | 2,063,300 | G→A | C8C (TGC→TGT) | ldtA ← | L,D‑transpeptidase ErfK |
| RA | 2,087,981 | T→C | N93S (AAC→AGC) | yeeY ← | putative DNA‑binding transcriptional regulator YeeY |
| RA | 2,170,193 | A→G | intergenic (‑26/‑43) | gatR ← / → insE‑5 | DNA‑binding transcriptional repressor GatR, N‑terminal fragment/IS3 element protein InsE |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,210,485 | G→A | R462R (CGG→CGA) | yehQ → | SWIM zinc finger domains‑containing protein YehQ |
| RA | 2,217,643 | T→C | L305L (TTA→TTG) | yehY ← | glycine betaine ABC transporter membrane subunit YehY |
| RA | 2,263,924 | (T)5→6 | coding (62/1182 nt) | setB → | sugar exporter SetB |
| RA | 2,264,341 | Δ1 bp | coding (479/1182 nt) | setB → | sugar exporter SetB |
| RA | 2,281,111 | G→A | W160* (TGG→TGA) | radD → | putative DNA repair helicase RadD |
| RA | 2,297,114 | (C)7→8 | coding (531/624 nt) | ccmA ← | heme trafficking system ATP‑binding protein |
| RA | 2,298,514 | G→A | H69Y (CAT→TAT) | napB ← | periplasmic nitrate reductase cytochrome c550 protein |
| RA | 2,351,149 | T→C | D409G (GAC→GGC) | glpT ← | sn‑glycerol 3‑phosphate:phosphate antiporter |
| RA | 2,381,437 | T→C | Y36C (TAT→TGT) | elaA ← | putative N‑acetyltransferase ElaA |
| RA | 2,386,814 | T→C | L319L (TTA→CTA) | yfbL → | putative peptidase YfbL |
| RA | 2,406,148 | T→C | N165S (AAC→AGC) | lrhA ← | DNA‑binding transcriptional dual regulator LrhA |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,462,889 | (C)9→10 | intergenic (+243/‑123) | fadL → / → yfdF | long‑chain fatty acid outer membrane channel/bacteriophage T2 receptor/protein YfdF |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,573,453 | A→G | V18A (GTT→GCT) | eutD ← | phosphate acetyltransferase EutD |
| RA | 2,623,319 | C→T | D92D (GAC→GAT) | ppk → | polyphosphate kinase |
| RA | 2,695,585 | (G)7→8 | intergenic (‑42/‑216) | purL ← / → mltF | phosphoribosylformylglycinamide synthetase/membrane‑bound lytic murein transglycosylase F |
| RA | 2,721,901 | T→C | V650A (GTT→GCT) | patZ → | peptidyl‑lysine acetyltransferase |
| RA | 2,723,976 | A→G | H417R (CAC→CGC) | pssA → | phosphatidylserine synthase |
| RA | 2,765,794 | (C)7→6 | intergenic (‑18/‑124) | yfjM ← / → rnlA | CP4‑57 prophage; protein YfjM/CP4‑57 prophage; RNase LS, toxin of the RnlAB toxin‑antitoxin system |
| RA | 2,773,381 | A→G | I22V (ATC→GTC) | yfjW → | CP4‑57 prophage; uncharacterized protein YfjW |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,831,026 | G→A | R422C (CGC→TGC) | norR ← | DNA‑binding transcriptional dual regulator NorR |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,882,486 | T→C | N51S (AAC→AGC) | casB ← | type I‑E CRISPR system Cascade subunit CasB |
| RA | 2,919,986 | A→G | V254A (GTT→GCT) | gudX ← | glucarate dehydratase‑related protein |
| RA | 2,928,846 | T→C | G206G (GGT→GGC) | sdaC → | serine:H(+) symporter SdaC |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,963,709 | A→G | V3A (GTA→GCA) *157Q (TAA→CAA) |
ppdB ← ppdA ← |
conserved protein PpdB conserved protein PpdA |
| RA | 2,989,120 | T→C | L207L (TTG→CTG) | yqeI → | putative transcriptional regulator YqeI |
| RA | 2,999,680 | (G)7→8 | coding (212/756 nt) | ygeR ← | LysM domain‑containing putative peptidase lipoprotein YgeR |
| RA | 3,001,304 | (G)7→9 | coding (960/2259 nt) | xdhA → | putative xanthine dehydrogenase molybdenum‑binding subunit XdhA |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,080,104 | T→C | D511G (GAC→GGC) | tktA ← | transketolase 1 |
| RA | 3,101,039 | (C)7→8 | coding (585/720 nt) | yggN ← | putative EcfF |
| RA | 3,106,772 | T→C | T353T (ACT→ACC) | nupG → | nucleoside:H(+) symporter NupG |
| RA | 3,134,578 | T→C | F150L (TTT→CTT) | yghT → | putative ATP‑binding protein YghT |
| RA | 3,195,218 | (G)6→7 | noncoding (23/144 nt) | sibE ← | small RNA SibE |
| RA | 3,214,360 | G→A | A438A (GCG→GCA) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 3,244,933 | T→C | intergenic (‑192/‑291) | uxaC ← / → exuT | D‑glucoronate/D‑galacturonate isomerase/hexuronate transporter |
| RA | 3,268,029 | T→C | V59A (GTA→GCA) | yhaB → | protein YhaB |
| RA | 3,273,769 | A→G | V380A (GTT→GCT) | garP ← | galactarate/glucarate/glycerate transporter GarP |
| RA | 3,280,344 | T→C | V43A (GTA→GCA) | agaV → | N‑acetyl‑D‑galactosamine specific PTS enzyme IIB component |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,432,994 | (C)6→5 | coding (567/1125 nt) | smf ← | protein Smf |
| RA | 3,452,160 | T→C | T43A (ACT→GCT) | rplD ← | 50S ribosomal subunit protein L4 |
| RA | 3,525,668 | T→C | D161G (GAC→GGC) | nudE ← | ADP‑sugar diphosphatase NudE |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,573,508 | T→C | intergenic (‑6/+267) | glgB ← / ← asd | 1,4‑alpha‑glucan branching enzyme/aspartate‑semialdehyde dehydrogenase |
| RA | 3,586,164 | G→A | D220D (GAC→GAT) | ggt ← | glutathione hydrolase proenzyme |
| RA | 3,659,898 | A→G | K223E (AAA→GAA) | mdtE → | multidrug efflux pump membrane fusion protein MdtE |
| RA | 3,753,234 | A→G | V289A (GTA→GCA) | yiaV ← | putative membrane fusion protein |
| RA | 3,781,358 | +G | coding (144/474 nt) | trmL → | tRNA (cytidine/uridine‑2'‑O)‑ribose methyltransferase |
| 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 | 3,911,606 | T→C | intergenic (‑81/+233) | pstS ← / ← glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| RA | 3,920,104 | A→G | R100R (CGT→CGC) | atpH ← | ATP synthase F1 complex subunit delta |
| RA | 3,961,591 | A→G | E305E (GAA→GAG) | rep → | ATP‑dependent DNA helicase Rep |
| RA | 3,982,684 | (C)8→9 | noncoding (79/87 nt) | leuT → | tRNA‑Leu |
| RA | 3,994,001 | C→T | R20H (CGC→CAC) A51V (GCG→GTG) |
cyaY ← yzcX → |
frataxin CyaY protein YzcX |
| RA | 4,177,613 | A→G | T86A (ACT→GCT) | secE → | Sec translocon subunit SecE |
| RA | 4,204,856 | A→G | V359A (GTG→GCG) | purD ← | phosphoribosylamine‑‑glycine ligase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,361,659 | A→G | T92T (ACT→ACC) | cadC ← | DNA‑binding transcriptional activator CadC |
| RA | 4,387,080 | A→G | V764A (GTC→GCC) | mscM ← | miniconductance mechanosensitive channel MscM |
| RA | 4,409,505 | A→G | G77G (GGA→GGG) | rlmB → | 23S rRNA 2'‑O‑ribose G2251 methyltransferase |
| RA | 4,424,463 | (C)5→6 | intergenic (+77/+53) | ulaF → / ← yjfY | L‑ribulose‑5‑phosphate 4‑epimerase UlaF/DUF1471 domain‑containing protein YjfY |
| RA | 4,431,450 | T→C | T178T (ACA→ACG) | ytfE ← | iron‑sulfur cluster repair protein YtfE |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,577,067 | (C)6→7 | coding (892/1047 nt) | mcrC ← | 5‑methylcytosine‑specific restriction enzyme subunit McrC |
| RA | 4,584,914 | A→G | A616A (GCT→GCC) | hsdR ← | type I restriction enzyme EcoKI endonuclease component |
| RA | 4,585,793 | C→T | R323R (AGG→AGA) | hsdR ← | type I restriction enzyme EcoKI endonuclease component |
| RA | 4,604,277 | A→G | T40A (ACC→GCC) | bglJ → | DNA‑binding transcriptional regulator BglJ |
| RA | 4,629,562 | C→T | D321N (GAT→AAT) | ettA ← | energy‑dependent translational throttle protein EttA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1432025–1432063 | 1432225–1432208 | 146–201 | 3 [2] | [1] 5 | stfR | Rac prophage; putative membrane protein |
| * | * | ÷ | NC_000913 | 1633759–1633921 | 1634968–1634641 | 721–1210 | 3 [2] | [2] 5 | [pinQ]–[ydfN] | [pinQ],tfaQ,[ydfN] |
| * | * | ÷ | NC_000913 | 3423770–3424233 | 3424520–3424239 | 7–751 | 3 [2] | [2] 3 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3943710–3943987 | 3945433–3944061 | 75–1724 | 3 [2] | [2] 3 | rrlC | 23S ribosomal RNA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 33 (1.340) | 7 (0.320) | 6/242 | 1.5 | 25.4% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 12 (0.550) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 3363001 = | 36 (1.460) | 35 (1.430) | 25/272 | 0.1 | 66.2% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 0 (0.000) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 27 (1.100) | 22/274 | 0.2 | 87.1% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 4 (0.160) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||