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 | 37,052 | A→G | V258A (GTA→GCA) | caiC ← | carnitine‑CoA ligase |
| RA | 61,200 | G→A | L689L (CTG→TTG) | rapA ← | RNA polymerase‑binding ATPase and RNAP recycling factor |
| RA | 88,006 | A→G | intergenic (+158/‑22) | ilvH → / → cra | acetolactate synthase/acetohydroxybutanoate synthase, regulatory subunit/DNA‑binding transcriptional dual regulator Cra |
| RA | 220,088 | A→G | intergenic (‑93/+25) | rcsF ← / ← metQ | outer membrane lipoprotein RcsF/L‑methionine/D‑methionine ABC transporter membrane anchored binding protein |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 268,466 | T→C | G165G (GGA→GGG) | ykfA ← | CP4‑6 prophage; putative GTP‑binding protein YkfA |
| RA | 321,565 | A→G | intergenic (+484/‑43) | rclR → / → ykgE | DNA‑binding transcriptional activator RclR/putative lactate utilization oxidoreductase YkgE |
| RA | 346,972 | G→A | A491V (GCT→GTT) | prpR ← | DNA‑binding transcriptional dual regulator PrpR |
| RA | 380,022 | (G)10→11 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 383,598 | (A)7→6 | coding (338/1197 nt) | yaiP ← | putative glucosyltransferase |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 531,195 | C→T | R11H (CGT→CAT) | selU ← | tRNA 2‑selenouridine synthase |
| RA | 534,550 | (G)5→6 | coding (635/1782 nt) | gcl → | glyoxylate carboligase |
| RA | 581,060 | A→T | D76V (GAT→GTT) | nohD → | DLP12 prophage; putative DNA‑packaging protein NohD |
| RA | 715,435 | C→T | V8V (GTC→GTT) | ybfP → | lipoprotein YbfP |
| RA | 723,528 | (T)8→7 | coding (887/2685 nt) | kdpD ← | sensory histidine kinase KdpD |
| RA | 730,654 | T→C | C358R (TGT→CGT) | rhsC → | rhs element protein RhsC |
| RA | 738,954 | A→G | intergenic (+101/‑47) | ybfD → / → ybgA | H repeat‑associated putative transposase YbfD/DUF1722 domain‑containing protein YbgA |
| RA | 799,146 | A→G | E187E (GAA→GAG) | pgl → | 6‑phosphogluconolactonase |
| RA | 802,524 | A→G | H213R (CAC→CGC) | ybhI → | putative tricarboxylate transporter |
| RA | 837,841 | A→G | S29P (TCC→CCC) | ybiJ ← | DUF1471 domain‑containing protein YbiJ |
| RA | 860,724 | A→G | L628P (CTG→CCG) | ybiW ← | putative pyruvate formate lyase |
| 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 |
| JC JC | 949,487 | IS5 (+) +4 bp | coding (79‑82/909 nt) | ycaN ← | putative LysR‑type transcriptional regulator YcaN |
| RA | 951,357 | A→G | V733A (GTA→GCA) | pflB ← | pyruvate formate‑lyase |
| RA | 989,044 | (G)6→7 | intergenic (‑59/+110) | asnS ← / ← pncB | asparagine‑‑tRNA ligase/nicotinate phosphoribosyltransferase |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,035,876 | C→T | P36L (CCC→CTC) | hyaD → | putative hydrogenase 1 maturation protease HyaD |
| RA | 1,092,303 | A→G | intergenic (‑14/‑573) | pgaA ← / → dgcT | partially deacetylated poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine outer membrane porin/putative diguanylate cyclase DgcT |
| RA | 1,097,580 | (G)7→8 | noncoding (73/88 nt) | serX ← | tRNA‑Ser |
| RA | 1,137,907 | Δ1 bp | coding (537/942 nt) | flgJ → | putative peptidoglycan hydrolase FlgJ |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,251,127 | A→G | E21G (GAG→GGG) | dhaR → | DNA‑binding transcriptional dual regulator DhaR |
| RA | 1,358,793 | A→G | V132A (GTG→GCG) | puuP ← | putrescine:H(+) symporter PuuP |
| RA | 1,360,535 | A→G | V125A (GTC→GCC) | puuA ← | glutamate‑putrescine ligase |
| RA | 1,399,978 | T→C | T87A (ACG→GCG) | ogt ← | methylated‑DNA‑‑[protein]‑cysteine S‑methyltransferase |
| RA | 1,420,793 | (G)6→7 | coding (110/423 nt) | ydaT → | Rac prophage; protein YdaT |
| RA | 1,466,816 | C→T | pseudogene (1425/2518 nt) | ydbA → | putative outer membrane protein, N‑terminal fragment |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,552,368 | 2 bp→TC | intergenic (+377/+29) | fdnI → / ← yddM | formate dehydrogenase N subunit gamma/putative DNA‑binding transcriptional regulator YddM |
| RA | 1,613,652 | A→G | V351A (GTT→GCT) | sad ← | NAD(+)‑dependent succinate semialdehyde dehydrogenase |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,682,066 | T→C | intergenic (‑36/‑93) | ydgC ← / → rstA | GlpM family protein/DNA‑binding transcriptional regulator RstA |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,793,850 | (C)6→7 | coding (260/552 nt) | btuE ← | thioredoxin/glutathione peroxidase |
| RA | 1,801,600 | T→C | N324S (AAC→AGC) | thrS ← | threonine‑‑tRNA ligase |
| RA | 1,816,479 | T→C | P219P (CCA→CCG) | chbG ← | chitin disaccharide deacetylase |
| RA | 1,873,384 | A→G | K448K (AAA→AAG) | dgcJ → | putative diguanylate cyclase DgcJ |
| RA | 1,876,158 | C→T | N162N (AAC→AAT) | 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 | 1,936,458 | T→C | intergenic (‑144/‑194) | zwf ← / → yebK | NADP(+)‑dependent glucose‑6‑phosphate dehydrogenase/DNA‑binding transcriptional repressor YebK |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,057,676 | (C)7→8 | intergenic (+102/+351) | yeeN → / ← asnW | putative transcriptional regulator YeeN/tRNA‑Asn |
| RA | 2,111,413 | A→G | G188G (GGT→GGC) | rfbD ← | dTDP‑4‑dehydrorhamnose reductase |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,177,409 | T→C | intergenic (‑205/+103) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,180,736 | A→G | S214S (TCA→TCG) | yegU → | putative ADP‑ribosylglycohydrolase YegU |
| RA | 2,185,875 | (G)7→8 | intergenic (‑79/‑42) | rcnR ← / → rcnA | DNA‑binding transcriptional repressor RcnR/Ni(2(+))/Co(2(+)) exporter |
| RA | 2,259,721 | A→G | *564Q (TAA→CAA) | fruA ← | fructose‑specific PTS multiphosphoryl transfer protein FruA |
| RA | 2,262,445 | T→C | T351A (ACC→GCC) | fruB ← | fructose‑specific PTS multiphosphoryl transfer protein FruB |
| RA | 2,317,536 | A→C | W781G (TGG→GGG) | rcsC ← | sensory histidine kinase RcsC |
| RA | 2,407,598 | T→C | V13A (GTC→GCC) | alaA → | glutamate‑‑pyruvate aminotransferase AlaA |
| RA | 2,417,658 | T→C | V193A (GTC→GCC) | yfcC → | putative transporter YfcC |
| 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 | 2,547,852 | T→C | F394L (TTT→CTT) | murP → | N‑acetylmuramic acid‑specific PTS enzyme IICB component/anhydro‑N‑acetylmuramic acid transporter |
| RA | 2,565,473 | T→C | intergenic (+141/+8) | yffS → / ← eutA | CPZ‑55 prophage; uncharacterized protein YffS/reactivating factor for ethanolamine ammonia‑lyase EutBC |
| RA | 2,605,854 | T→C | G348G (GGT→GGC) | hyfD → | hydrogenase 4 component D |
| RA | 2,623,206 | G→A | A55T (GCT→ACT) | ppk → | polyphosphate kinase |
| RA | 2,656,399 | C→T | intergenic (‑41/+137) | pepB ← / ← iscX | aminopeptidase B/accessory iron‑sulfur cluster assembly protein IscX |
| RA | 2,695,585 | (G)7→8 | intergenic (‑42/‑216) | purL ← / → mltF | phosphoribosylformylglycinamide synthetase/membrane‑bound lytic murein transglycosylase F |
| RA | 2,701,540 | T→C | T64A (ACG→GCG) | pdxJ ← | pyridoxine 5'‑phosphate synthase |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,813,230 | Δ1 bp | coding (615/1539 nt) | emrB → | multidrug efflux pump membrane subunit EmrB |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,860,837 | T→C | N133S (AAC→AGC) | ygbI ← | putative DeoR‑type DNA‑binding transcriptional regulator YgbI |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,092,566 | (G)6→5 | coding (689/951 nt) | gshB → | glutathione synthetase |
| RA | 3,105,846 | A→G | S45G (AGC→GGC) | nupG → | nucleoside:H(+) symporter NupG |
| RA | 3,138,363 | C→T | G54S (GGC→AGC) | gss ← | fused glutathionylspermidine amidase/glutathionylspermidine synthetase |
| RA | 3,144,425 | T→C | Y239C (TAC→TGC) | hybA ← | hydrogenase 2 iron‑sulfur protein |
| RA | 3,188,683 | T→C | pseudogene (1252/2434 nt) | yqiG → | putative outer membrane usher protein YqiG |
| RA | 3,208,044 | G→A | W7* (TGG→TGA) | ttdT → | L‑tartrate:succinate antiporter |
| RA | 3,209,542 | T→C | L334L (TTA→TTG) | tsaD ← | N(6)‑L‑threonylcarbamoyladenine synthase, TsaD subunit |
| RA | 3,216,364 | T→C | D43G (GAC→GGC) | nfeF ← | NADPH‑dependent ferric chelate reductase |
| RA | 3,254,028 | A→G | F63L (TTC→CTC) | yhaJ ← | DNA‑binding transcriptional activator YhaJ |
| RA | 3,278,978 | T→C | V22A (GTT→GCT) | kbaZ → | tagatose‑1,6‑bisphosphate aldolase 1 subunit KbaZ |
| 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 | 3,401,949 | G→A | R462C (CGT→TGT) | csrD ← | regulator of CsrB and CsrC decay |
| RA | 3,419,129 | C→T | pseudogene (88/1025 nt) | yhdW → | putative ABC transporter periplasmic binding protein YhdW |
| RA | 3,430,330 | G→A | A170V (GCG→GTG) | aroE ← | shikimate dehydrogenase |
| RA | 3,450,397 | T→C | M44V (ATG→GTG) | rpsS ← | 30S ribosomal subunit protein S19 |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,597,156 | T→C | Q135Q (CAA→CAG) | livK ← | L‑leucine/L‑phenylalanine ABC transporter periplasmic binding protein |
| RA | 3,801,128 | (G)5→6 | coding (872/1017 nt) | waaJ ← | UDP‑glucose:(glucosyl)LPS alpha‑1,2‑glucosyltransferase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,856,604 | (A)6→5 | coding (190/450 nt) | yidI → | putative inner membrane protein |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,915,448 | (G)6→7 | intergenic (‑248/+105) | glmU ← / ← atpC | fused N‑acetylglucosamine‑1‑phosphate uridyltransferase and glucosamine‑1‑phosphate acetyltransferase/ATP synthase F1 complex subunit epsilon |
| RA | 4,130,215 | C→T | G127G (GGC→GGT) | metL → | fused aspartate kinase/homoserine dehydrogenase 2 |
| RA | 4,132,292 | T→C | intergenic (+25/‑324) | metL → / → metF | fused aspartate kinase/homoserine dehydrogenase 2/5,10‑methylenetetrahydrofolate reductase |
| RA | 4,197,774 | T→C | V20A (GTC→GCC) | hemE → | uroporphyrinogen decarboxylase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,344,595 | T→C | G409G (GGT→GGC) | melB → | melibiose:H(+)/Na(+)/Li(+) symporter |
| RA | 4,414,445 | A→G | E57E (GAA→GAG) | aidB → | putative acyl‑CoA dehydrogenase AidB |
| RA | 4,421,194 | T→C | S405S (AGT→AGC) | ulaA → | L‑ascorbate specific PTS enzyme IIC component |
| RA | 4,425,689 | A→G | H57R (CAC→CGC) | priB → | primosomal replication protein N |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,446,443 | C→T | R778C (CGT→TGT) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,448,907 | C→T | G72G (GGC→GGT) | chpB → | endoribonuclease toxin ChpB |
| RA | 4,545,134 | A→G | T13T (ACA→ACG) | fimD → | type I fimbriae usher protein |
| RA | 4,556,328 | A→G | intergenic (‑8/‑246) | yjiC ← / → ytiC | uncharacterized protein YjiC/protein YtiC |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 730658 | 731498 | 841 | 24 [20] | [19] 21 | rhsC | rhs element protein RhsC |
| * | * | ÷ | NC_000913 | 732439 | 732913–732605 | 167–475 | 21 [20] | [19] 21 | rhsC | rhs element protein RhsC |
| * | * | ÷ | NC_000913 | 1552135–1552184 | 1552306–1552213 | 30–172 | 25 [17] | [20] 21 | fdnI/yddM | formate dehydrogenase N subunit gamma/putative DNA‑binding transcriptional regulator YddM |
| * | * | ÷ | NC_000913 | 3423770–3424234 | 3424526–3424238 | 5–757 | 24 [18] | [18] 21 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 78 (0.990) | 56/268 | 0.2 | 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 = | 120 (1.490) | 124 (1.550) | 68/274 | 0.1 | 66.5% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 6 (0.070) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 90 (1.110) | 52/276 | 0.3 | 97.8% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 2 (0.020) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||