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 | 12,020 | A→G | intergenic (‑234/‑143) | yaaI ← / → dnaK | DUF2541 domain‑containing protein YaaI/chaperone protein DnaK |
| RA | 31,834 | A→G | T340A (ACT→GCT) | carB → | carbamoyl phosphate synthetase subunit beta |
| RA | 56,246 | T→C | E288E (GAA→GAG) | lptD ← | lipopolysaccharide assembly protein LptD |
| RA | 61,038 | A→G | S743P (TCC→CCC) | rapA ← | RNA polymerase‑binding ATPase and RNAP recycling factor |
| RA | 96,252 | T→C | V84A (GTG→GCG) | mraY → | phospho‑N‑acetylmuramoyl‑pentapeptide‑ transferase |
| RA | 118,198 | A→G | L150L (TTG→CTG) | nadC ← | quinolinate phosphoribosyltransferase (decarboxylating) |
| RA | 125,718 | G→A | P8P (CCG→CCA) | aceF → | pyruvate dehydrogenase, E2 subunit |
| RA | 152,988 | T→C | Q813Q (CAA→CAG) | htrE ← | putative fimbrial usher protein HtrE |
| RA | 187,029 | A→G | L541P (CTG→CCG) | glnD ← | PII uridylyltransferase/uridylyl removing enzyme |
| RA | 209,600 | A→G | intergenic (+20/‑79) | accA → / → ldcC | acetyl‑CoA carboxyltransferase subunit alpha/lysine decarboxylase 2 |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 273,785 | A→G | K313K (AAA→AAG) | ykfC → | CP4‑6 prophage; PF00078 domain‑containing protein YkfC |
| RA | 281,950 | T→C | T12A (ACC→GCC) | yagA ← | CP4‑6 prophage; integrase core domain‑containing protein YagA |
| RA | 285,561 | A→G | D56G (GAC→GGC) | yagG → | putative D‑xylonate transporter YagG |
| RA | 287,351 | C→T | A188V (GCG→GTG) | yagH → | CP4‑6 prophage; putative xylosidase/arabinosidase |
| RA | 309,752 | A→G | V92A (GTG→GCG) | ecpB ← | putative fimbrial chaperone EcpB |
| JC | 380,020 | (G)10→7 | intergenic (‑139/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 380,022 | (G)10→11 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 457,810 | G→A | A129T (GCT→ACT) | clpX → | ATP‑dependent Clp protease ATP‑binding subunit ClpX |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 529,029 | C→T | pseudogene (390/491 nt) | ybbD → | putative uncharacterized protein YbbD |
| RA | 542,227 | A→G | T114A (ACG→GCG) | glxK → | glycerate 2‑kinase 2 |
| RA | 554,581 | T→C | intergenic (‑144/‑30) | ppiB ← / → cysS | peptidyl‑prolyl cis‑trans isomerase B/cysteine‑‑tRNA ligase |
| RA | 560,056 | C→T | P120P (CCC→CCT) | sfmD → | putative fimbrial usher protein SfmD |
| RA | 603,772 | G→A | R298C (CGC→TGC) | ybdG ← | miniconductance mechanosensitive channel YbdG |
| RA | 679,793 | T→G | L96V (TTG→GTG) | ybeU → | DUF1266 domain‑containing protein YbeU |
| RA | 766,957 | (G)6→7 | coding (974/1977 nt) | mngA → | 2‑O‑alpha‑mannosyl‑D‑glycerate specific PTS enzyme II |
| 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 | 961,344 | A→G | L48L (TTA→TTG) | cmk → | cytidylate kinase |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,029,739 | (A)8→7 | coding (231/1191 nt) | rlmI ← | 23S rRNA m(5)C1962 methyltransferase |
| RA | 1,066,904 | (A)6→7 | coding (188/228 nt) | yccJ ← | PF13993 family protein YccJ |
| RA | 1,073,080 | T→A | D311V (GAT→GTT) | rutA ← | pyrimidine oxygenase |
| RA | 1,073,492 | A→G | W174R (TGG→CGG) | rutA ← | pyrimidine oxygenase |
| RA | 1,097,037 | (G)7→8 | intergenic (+208/+528) | ycdU → / ← serX | uncharacterized protein YcdU/tRNA‑Ser |
| RA | 1,100,062 | A→G | L141L (TTA→TTG) | ycdY → | chaperone protein YcdY |
| RA | 1,137,693 | C→T | S108F (TCC→TTC) | flgJ → | putative peptidoglycan hydrolase FlgJ |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,162,592 | (G)5→6 | coding (346/378 nt) | ycfL → | DUF1425 domain‑containing protein YcfL |
| RA | 1,212,088 | (C)8→9 | intergenic (‑85/+172) | iraM ← / ← ymgK | anti‑adaptor protein IraM, inhibitor of sigma(S) proteolysis/protein YmgK |
| RA | 1,219,925 | A→G | pseudogene (325/2648 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 | 1,269,250 | A→G | I9T (ATT→ACT) | ldrA ← | small toxic polypeptide LdrA |
| RA | 1,269,362 | G→T | noncoding (40/67 nt) | rdlA → | putative antisense RNA regulator of LdrA |
| RA | 1,324,319 | A→G | E74E (GAA→GAG) | yciO → | putative RNA‑binding protein YciO |
| RA | 1,345,138 | A→G | C535C (TGT→TGC) | pdeR ← | cyclic di‑GMP phosphodiesterase PdeR |
| RA | 1,361,613 | (G)6→7 | coding (494/765 nt) | puuD → | gamma‑glutamyl‑gamma‑aminobutyrate hydrolase |
| RA | 1,370,044 | (T)9→8 | intergenic (+41/‑172) | pspE → / → ycjM | thiosulfate sulfurtransferase PspE/glucosylglycerate phosphorylase |
| RA | 1,373,436 | C→T | S72L (TCG→TTG) | ycjO → | putative ABC transporter membrane subunit YcjO |
| RA | 1,399,871 | A→G | R122R (CGT→CGC) | ogt ← | methylated‑DNA‑‑[protein]‑cysteine S‑methyltransferase |
| RA | 1,421,638 | (C)7→8 | coding (520/858 nt) | ydaU → | Rac prophage; DUF1376 domain‑containing protein YdaU |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,572,722 | A→G | C827C (TGT→TGC) | pqqL ← | putative zinc peptidase |
| RA | 1,575,020 | C→T | W61* (TGG→TGA) | pqqL ← | putative zinc peptidase |
| RA | 1,577,263 | T→C | P119P (CCA→CCG) | yddB ← | putative TonB‑dependent receptor |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,640,376 | T→C | G70G (GGA→GGG) | essQ ← | Qin prophage; putative S lysis protein |
| RA | 1,647,725 | A→G | R42R (CGT→CGC) | dicC ← | Qin prophage; DNA‑binding transcriptional regulator for DicB |
| 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 | 1,724,478 | (G)6→7 | coding (178/522 nt) | sodC ← | superoxide dismutase (Cu‑Zn) |
| RA | 1,725,250 | T→C | H128R (CAC→CGC) | ydhF ← | putative oxidoreductase |
| RA | 1,769,479 | A→G | T136A (ACG→GCG) | ydiK → | putative transporter YdiK |
| RA | 1,821,724 | G→A | intergenic (‑105/+194) | chbB ← / ← osmE | N,N'‑diacetylchitobiose‑specific PTS enzyme IIB component/osmotically‑inducible lipoprotein OsmE |
| RA | 1,823,865 | T→C | C117C (TGT→TGC) | cho → | endonuclease of nucleotide excision repair |
| RA | 1,871,162 | A→G | T260A (ACA→GCA) | cdgI → | putative c‑di‑GMP binding protein CdgI |
| RA | 1,873,384 | A→G | K448K (AAA→AAG) | dgcJ → | putative diguanylate cyclase DgcJ |
| RA | 1,877,900 | G→A | M62I (ATG→ATA) | dgcP → | diguanylate cyclase DgcP |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,017,429 | (C)6→7 | coding (876/1374 nt) | fliI → | flagellum‑specific ATP synthase FliI |
| RA | 2,025,705 | T→C | G65G (GGT→GGC) | yedP → | putative mannosyl‑3‑phosphoglycerate phosphatase |
| RA | 2,060,362 | T→C | T185A (ACG→GCG) | cbl ← | DNA‑binding transcriptional activator Cbl |
| RA | 2,078,456 | (A)6→7 | intergenic (+322/‑119) | yeeW → / → yoeF | CP4‑44 prophage; putative uncharacterized protein YeeW/CP4‑44 prophage; putative uncharacterized protein YoeF |
| RA | 2,099,811 | (A)8→9 | intergenic (‑198/+51) | ugd ← / ← gnd | UDP‑glucose 6‑dehydrogenase/6‑phosphogluconate dehydrogenase, decarboxylating |
| RA | 2,162,896 | T→C | G7G (GGT→GGC) | baeS → | sensory histidine kinase BaeS |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,217,643 | T→C | L305L (TTA→TTG) | yehY ← | glycine betaine ABC transporter membrane subunit YehY |
| RA | 2,222,243 | T→C | V20A (GTG→GCG) | dld → | D‑lactate dehydrogenase |
| RA | 2,225,733 | T→C | intergenic (‑102/‑68) | yohC ← / → yohD | putative inner membrane protein/DedA family protein YohD |
| RA | 2,226,052 | G→A | A84A (GCG→GCA) | yohD → | DedA family protein YohD |
| RA | 2,249,622 | C→T | intergenic (‑4/‑95) | yeiE ← / → yeiH | putative LysR‑type transcriptional regulator YeiE/conserved inner membrane protein YeiH |
| RA | 2,277,598 | T→C | R433R (CGT→CGC) | yejF → | putative oligopeptide ABC transporter ATP binding subunit |
| RA | 2,338,723 | T→C | Y233C (TAC→TGC) | gyrA ← | DNA gyrase subunit A |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,471,489 | T→C | N10S (AAC→AGC) | yfdK ← | CPS‑53 (KpLE1) prophage; putative tail fiber assembly protein YfdK |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,609,038 | C→T | I184I (ATC→ATT) | hyfG → | hydrogenase 4 catalytic subunit HyfG |
| RA | 2,659,669 | T→C | D73G (GAC→GGC) | iscA ← | iron‑sulfur cluster insertion protein IscA |
| RA | 2,706,133 | G→A | S331F (TCC→TTC) | lepA ← | elongation factor 4 |
| RA | 2,719,833 | A→G | E204G (GAG→GGG) | yfiP → | conserved protein YfiP |
| RA | 2,734,543 | (C)8→9 | coding (492/732 nt) | pgeF ← | polyphenol oxidase YfiH |
| RA | 2,738,867 | T→C | Y375H (TAC→CAC) | pheA → | fused chorismate mutase/prephenate dehydratase |
| RA | 2,744,734 | G→A | A202A (GCC→GCT) | trmD ← | tRNA m(1)G37 methyltransferase |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,824,478 | (C)6→5 | intergenic (‑132/+13) | pncC ← / ← mltB | NMN aminohydrolase/membrane‑bound lytic murein transglycosylase B |
| RA | 2,844,631 | A→G | I41T (ATC→ACC) | hycF ← | formate hydrogenlyase subunit HycF |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,867,918 | T→C | N279S (AAC→AGC) | nlpD ← | murein hydrolase activator NlpD |
| RA | 2,879,516 | T→C | Y86C (TAT→TGT) | cas1 ← | multifunctional nuclease Cas1 |
| RA | 2,935,327 | T→C | Y365H (TAC→CAC) | fucP → | L‑fucose:H(+) symporter |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,971,669 | G→A | E25K (GAA→AAA) | tas → | putative NADP(H)‑dependent aldo‑keto reductase Tas |
| RA | 3,002,255 | T→C | N637N (AAT→AAC) | xdhA → | putative xanthine dehydrogenase molybdenum‑binding subunit XdhA |
| RA | 3,022,559 | T→C | V415A (GTA→GCA) | xdhD → | fused putative xanthine/hypoxanthine oxidase: molybdopterin‑binding subunit and Fe‑S binding subunit |
| RA | 3,026,663 | A→G | T300A (ACC→GCC) | guaD → | guanine deaminase |
| RA | 3,056,402 | A→G | E54E (GAA→GAG) | fau → | putative 5‑formyltetrahydrofolate cyclo‑ligase |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,074,131 | T→C | S187G (AGT→GGT) | yggC ← | P‑loop NTPase domain‑containing protein YggC |
| RA | 3,117,194 | T→C | Q640R (CAG→CGG) | yghJ ← | putative lipoprotein YghJ |
| RA | 3,270,488 | (C)7→8 | noncoding (105/377 nt) | rnpB ← | RNase P catalytic RNA component |
| RA | 3,301,492 | T→C | L3P (CTG→CCG) | yhbU → | putative peptidase YhbU |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,357,547 | C→T | G941G (GGC→GGT) | gltB → | glutamate synthase subunit GltB |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,463,808 | T→C | S295S (AGT→AGC) | gspK → | Type II secretion system protein GspK |
| RA | 3,548,915 | T→C | T386A (ACC→GCC) | malQ ← | 4‑alpha‑glucanotransferase |
| RA | 3,549,305 | T→C | T256A (ACC→GCC) | malQ ← | 4‑alpha‑glucanotransferase |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,593,991 | T→C | L72L (TTA→TTG) | livG ← | branched chain amino acid/phenylalanine ABC transporter ATP binding subunit LivG |
| RA | 3,643,336 | Δ1 bp | coding (1847/2043 nt) | prlC ← | oligopeptidase A |
| RA | 3,736,884 | T→C | E98E (GAA→GAG) | bax ← | putative glycoside hydrolase Bax |
| RA | 3,749,860 | T→C | L210P (CTG→CCG) | sgbU → | putative L‑xylulose 5‑phosphate 3‑epimerase |
| RA | 3,775,191 | T→C | G256G (GGT→GGC) | mtlD → | mannitol‑1‑phosphate 5‑dehydrogenase |
| RA | 3,781,355 | G→A | A47A (GCG→GCA) | 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 | 3,865,335 | T→C | E313E (GAA→GAG) | yidE ← | putative transport protein YidE |
| RA | 3,889,662 | A→G | E311E (GAA→GAG) | tnaA → | tryptophanase |
| RA | 3,922,067 | T→C | K125R (AAA→AGA) | atpI ← | ATP synthase accessory factor |
| RA | 3,951,311 | A→G | pseudogene (752/1645 nt) | ilvG → | acetolactate synthase II subunit IlvG, N‑terminal fragment (pseudogene) |
| RA | 4,122,367 | (G)7→8 | intergenic (‑80/+13) | hslV ← / ← ftsN | peptidase component of the HslVU protease/cell division protein FtsN |
| RA | 4,239,087 | A→G | D485G (GAC→GGC) | yjbH → | YjbH family protein |
| RA | 4,270,070 | A→G | K219K (AAA→AAG) | aphA → | acid phosphatase/phosphotransferase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,333,372 | A→G | H193H (CAT→CAC) | basR ← | DNA‑binding transcriptional dual regulator BasR |
| RA | 4,410,053 | (T)9→8 | intergenic (+47/‑80) | rlmB → / → yjfI | 23S rRNA 2'‑O‑ribose G2251 methyltransferase/conserved protein YjfI |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,446,348 | C→T | T746I (ACC→ATC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,536,171 | G→A | intergenic (+140/+443) | yjhR → / ← nanS | KpLE2 phage‑like element; PLD‑like domain‑containing protein YjhR/N‑acetyl‑9‑O‑acetylneuraminate esterase |
| RA | 4,552,826 | A→G | intergenic (+6/‑75) | uxuA → / → uxuB | D‑mannonate dehydratase/D‑mannonate oxidoreductase |
| RA | 4,562,963 | (T)7→8 | coding (641/861 nt) | yjiK ← | uncharacterized protein YjiK |
| RA | 4,581,419 | A→G | V15A (GTA→GCA) | hsdS ← | type I restriction enzyme EcoKI specificity protein |
| RA | 4,589,756 | A→G | G508G (GGT→GGC) | btsT ← | pyruvate:H(+) symporter |
| RA | 4,590,908 | (C)5→7 | coding (372/2151 nt) | btsT ← | pyruvate:H(+) symporter |
| RA | 4,606,215 | (G)8→9 | noncoding (72/87 nt) | leuP ← | tRNA‑Leu |
| RA | 4,615,011 | (C)5→6 | coding (533/864 nt) | yjjW ← | putative glycyl‑radical enzyme activating enzyme YjjW |
| RA | 4,628,537 | A→G | E408G (GAG→GGG) | nadR → | DNA‑binding transcriptional repressor/NMN adenylyltransferase NadR |
| RA | 4,632,628 | A→G | K632K (AAA→AAG) | slt → | soluble lytic murein transglycosylase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 732684–732951 | 734592–734476 | 1526–1909 | 13 [10] | [10] 13 | [rhsC]–[ybfO] | [rhsC],ybfB,[ybfO] |
| * | * | ÷ | NC_000913 | 2066303–2066464 | 2066582–2066466 | 3–280 | 13 [12] | [7] 14 | [insH‑6] | [insH‑6] |
| * | * | ÷ | NC_000913 | 3423766–3424233 | 3424523–3424239 | 7–758 | 13 [12] | [12] 14 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 374963 | NA (NA) | 8 (0.210) | 7/188 | 2.8 | NA | noncoding (33/34 nt) | other | REP31a |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 57 (1.060) | 40/266 | 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 = | 78 (1.410) | 107 (1.950) | 58/272 | 0.0 | 73.4% | 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) | 61 (1.110) | 41/274 | 0.2 | 96.8% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 2 (0.040) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 4542690 | 24 (0.430) | 12 (0.230) | 10/256 | 2.9 | 30.2% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 33 (0.640) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||