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 | freq | annotation | gene | description |
| RA | 393,383 | C→T | 100% | A19V (GCG→GTG) | yaiW → | putative lipoprotein |
| RA | 427,459:1 | +T | 100% | coding (11/885 nt) | tsx ← | nucleoside channel, receptor of phage T6 and colicin K |
| RA | 451,541 | C→T | 100% | A318V (GCT→GTT) | tig → | peptidyl‑prolyl cis/trans isomerase (trigger factor) |
| RA | 481,297 | Δ1 bp | 100% | coding (81/648 nt) | acrR → | transcriptional repressor |
| RA | 663,969 | C→T | 100% | R68H (CGC→CAC) | rlmH ← | 23S rRNA m(3)Psi1915 pseudouridine methyltransferase, SAM‑dependent |
| JC | 670,239 | +GGCAGC | 100% | coding (1/2583 nt) | leuS ← | leucyl‑tRNA synthetase |
| RA | 804,210 | G→A | 100% | Y168Y (TAC→TAT) | bioA ← | 7,8‑diaminopelargonic acid synthase, PLP‑dependent |
| RA | 858,969 | G→C | 7.8% | intergenic (‑2/‑129) | ybiY ← / → fsaA | putative pyruvate formate lyase activating enzyme/fructose‑6‑phosphate aldolase 1 |
| RA | 982,211 | Δ1 bp | 100% | coding (228/1089 nt) | ompF ← | outer membrane porin 1a (Ia;b;F) |
| RA | 982,213 | C→G | 100% | D76H (GAT→CAT) | ompF ← | outer membrane porin 1a (Ia;b;F) |
| RA | 986,278 | T→C | 100% | N67N (AAT→AAC) | pepN → | aminopeptidase N |
| RA | 997,673:1 | +G | 100% | coding (411/1071 nt) | elfG → | putative fimbrial‑like adhesin protein |
| RA | 1,175,774 | G→A | 100% | E230K (GAA→AAA) | cobB → | deacetylase of acs and cheY, chemotaxis regulator |
| RA | 1,264,315 | G→C | 100% | G232A (GGT→GCT) | kdsA → | 3‑deoxy‑D‑manno‑octulosonate 8‑phosphate synthase |
| RA | 1,279,784 | A→G | 100% | E242G (GAG→GGG) | narH → | nitrate reductase 1, beta (Fe‑S) subunit |
| RA | 1,324,803 | G→A | 32.8% | G41G (GGC→GGT) | yciN ← | DUF2498 protein YciN |
| RA | 1,592,701 | T→C | 100% | intergenic (‑457/+173) | yneO ← / ← lsrK | pseudogene, AidA homolog/autoinducer‑2 (AI‑2) kinase |
| RA | 1,613,556:1 | +A | 100% | coding (180/435 nt) | marR → | transcriptional repressor of multiple antibiotic resistance |
| RA | 1,629,345 | T→C | 100% | T254A (ACA→GCA) | stfQ ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,642,091 | G→A | 100% | A6V (GCT→GTT) | dicC ← | Qin prophage; DNA‑binding transcriptional regulator for DicB |
| RA | 1,683,636 | C→T | 100% | N268N (AAC→AAT) | manA → | mannose‑6‑phosphate isomerase |
| RA | 1,693,582 | T→C | 32.6% | intergenic (‑145/‑30) | malI ← / → malX | transcriptional repressor of Mal regulon/fused maltose and glucose‑specific PTS enzymes: IIB component, IIC component |
| RA | 1,716,100 | T→C | 100% | F194L (TTT→CTT) | ydhJ → | putative membrane fusion protein (MFP) of YdhJK efflux pump |
| RA | 1,737,714 | G→A | 100% | M1M (GTG→ATG) † | mdtK → | multidrug efflux system transporter |
| RA | 1,738,557 | T→G | 100% | S282A (TCA→GCA) | mdtK → | multidrug efflux system transporter |
| RA | 2,059,881 | A→G | 100% | L308L (TTG→CTG) | insH1 ← | IS5 transposase and trans‑activator |
| RA | 2,059,915 | T→C | 100% | R296R (CGA→CGG) | insH1 ← | IS5 transposase and trans‑activator |
| RA | 2,121,147 | A→G | 100% | Y217H (TAC→CAC) | gmd ← | GDP‑D‑mannose dehydratase, NAD(P)‑binding |
| RA | 2,173,391 | G→A | 100% | M364I (ATG→ATA) | yegT → | nucleoside transporter, low affinity |
| RA | 2,306,235 | A→G | 22.7% | intergenic (‑7/‑328) | ompC ← / → micF | outer membrane porin protein C/sRNA antisense regulator affecting ompF expression, Hfq‑dependent |
| RA | 2,307,414 | G→A | 100% | G150S (GGT→AGT) | rcsD → | phosphotransfer intermediate protein in two‑component regulatory system with RcsBC |
| RA | 2,312,875 | G→T | 100% | R161S (CGT→AGT) | rcsC ← | hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| RA | 2,315,438 | C→T | 100% | H32Y (CAT→TAT) | atoC → | fused response regulator of ato operon, in two‑component system with AtoS: response regulator/sigma54 interaction protein |
| MC JC | 2,332,651 | Δ3 bp | 100% | coding (247‑249/2628 nt) | gyrA ← | DNA gyrase (type II topoisomerase), subunit A |
| RA | 2,372,258 | C→T | 100% | A161T (GCG→ACG) | menD ← | 2‑succinyl‑5‑enolpyruvyl‑6‑hydroxy‑3‑ cyclohexene‑1‑carboxylate synthase; SEPHCHC synthase |
| RA | 2,503,917 | T→C | 100% | I270T (ATT→ACT) | yfeO → | putative ion channel protein |
| RA | 2,553,692 | Δ1 bp | 100% | coding (77/642 nt) | yffL → | CPZ‑55 prophage; uncharacterized protein |
| RA | 2,613,559:1 | +A | 100% | intergenic (‑40/+46) | uraA ← / ← upp | uracil permease/uracil phosphoribosyltransferase |
| RA | 2,668,866 | A→G | 10.8% | H85H (CAT→CAC) | yphC ← | putative Zn‑dependent NAD(P)‑binding oxidoreductase |
| RA | 2,697,104 | G→A | 22.9% | R107C (CGT→TGT) | rnc ← | RNase III |
| RA | 2,705,225 | G→A | 100% | V483I (GTC→ATC) | nadB → | quinolinate synthase, L‑aspartate oxidase (B protein) subunit |
| RA | 2,760,798 | Δ1 bp | 100% | intergenic (+84/‑271) | rnlB → / → yfjP | CP4‑57 prophage; uncharacterized protein/CP4‑57 prophage; 50S ribosome‑binding GTPase family protein |
| RA | 2,969,704 | T→C | 100% | noncoding (41/82 nt) | omrB ← | sRNA antisense regulator downregulates OM proteins and curli; positively regulated by OmpR/EnvZ, Hfq‑dependent |
| RA | 3,070,486 | T→C | 33.2% | E110E (GAA→GAG) | yggP ← | putative Zn‑binding dehydrogenase |
| RA | 3,085,920 | Δ1 bp | 100% | coding (684/951 nt) | gshB → | glutathione synthetase |
| RA | 3,167,384 | A→G | 100% | S458P (TCG→CCG) | parE ← | DNA topoisomerase IV, subunit B |
| RA | 3,185,939 | T→C | 100% | W125R (TGG→CGG) | yqiJ → | DUF1449 family inner membrane protein |
| RA | 3,207,735 | G→A | 100% | A444T (GCG→ACG) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 3,210,117 | A→G | 100% | intergenic (‑267/‑21) | yqjH ← / → yqjI | putative siderophore interacting protein/PadR family putative transcriptional regulator |
| RA | 3,249,774 | C→T | 15.4% | A79A (GCG→GCA) | yhaM ← | putative L‑serine dehydratase alpha chain |
| RA | 3,267,827 | C→T | 100% | G147D (GGT→GAT) | garP ← | putative (D)‑galactarate transporter |
| RA | 3,442,737 | C→T | 20.8% | R169H (CGC→CAC) | rpsC ← | 30S ribosomal subunit protein S3 |
| RA | 3,444,573 | T→C | 100% | T51A (ACT→GCT) | rplB ← | 50S ribosomal subunit protein L2 |
| RA | 3,678,827 | Δ1 bp | 17.1% | coding (152/1989 nt) | yhjK ← | cyclic‑di‑GMP phosphodiesterase |
| RA | 3,744,943 | C→T | 10.2% | A96T (GCC→ACC) | yiaT ← | putative outer membrane protein |
| RA | 3,786,289 | T→C | 100% | N252S (AAC→AGC) | yibB ← | YibB family protein, function unknown |
| RA | 3,827,782:1 | +G | 100% | coding (116/2319 nt) | yicI ← | putative alpha‑glucosidase |
| RA | 3,872,086 | T→C | 100% | Q465R (CAG→CGG) | gyrB ← | DNA gyrase, subunit B |
| RA | 3,922,682 | C→T | 100% | Q94Q (CAG→CAA) | viaA ← | stimulator of RavA ATPase activity; von Willebrand factor domain protein |
| RA | 3,931,365 | C→T | 100% | Q238* (CAG→TAG) | rbsK → | ribokinase |
| RA | 3,976,036:1 | +C | 100% | noncoding (71/87 nt) | leuT → | tRNA‑Leu |
| RA | 4,021,068 | C→T | 100% | T355T (ACG→ACA) | fadA ← | 3‑ketoacyl‑CoA thiolase (thiolase I) |
| RA | 4,194,485 | C→A | 15.7% | A413E (GCG→GAG) | zraR → | fused DNA‑binding response regulator in two‑component regulatory system with ZraS: response regulator/sigma54 interaction protein |
| RA | 4,277,030 | G→A | 100% | G90G (GGC→GGT) | acs ← | acetyl‑CoA synthetase |
| RA | 4,278,884 | G→A | 100% | G398D (GGT→GAT) | nrfA → | nitrite reductase, formate‑dependent, cytochrome |
| RA | 4,294,396:1 | +G | 100% | intergenic (‑176/+33) | ytcA ← / ← yjcS | putative inner membrane DUF1656 family protein; efflux pump associated/metallo‑beta‑lactamase superfamily protein |
| MC JC | 4,388,448 | Δ13 bp | 100% | coding (1220‑1232/1848 nt) | mutL → | methyl‑directed mismatch repair protein |
| RA | 4,412,635 | C→T | 10.5% | I211I (ATC→ATT) | ulaD → | 3‑keto‑L‑gulonate 6‑phosphate decarboxylase |
| RA | 4,421,070 | C→T | 100% | R464W (CGG→TGG) | cycA → | D‑alanine/D‑serine/glycine transporter |
| RA | 4,435,602 | T→C | 100% | G558G (GGT→GGC) | tamB → | translocation and assembly module for autotransporter export, inner membrane subunit |
| RA | 4,519,981 | A→G | 100% | I27T (ATC→ACC) | sgcC ← | putative PTS system EIIC permease component |
| RA | 4,546,578 | Δ1 bp | 100% | intergenic (‑441/‑232) | yjiC ← / → iraD | uncharacterized protein/RpoS stabilzer after DNA damage, anti‑RssB factor |
| RA | 4,568,151 | G→A | 100% | A335V (GCC→GTC) | mcrB ← | 5‑methylcytosine‑specific restriction enzyme McrBC, subunit McrB |
| RA | 4,595,903:1 | +G | 100% | noncoding (80/87 nt) | leuV ← | tRNA‑Leu |
| RA | 4,596,033 | A→G | 100% | noncoding (71/87 nt) | leuP ← | tRNA‑Leu |
| RA | 4,596,139:1 | +G | 100% | noncoding (80/87 nt) | leuQ ← | tRNA‑Leu |
| RA | 4,602,935 | C→T | 100% | V236V (GTC→GTT) | yjjU → | putative patatin‑like family phospholipase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 266370–267005 | 289221 | 22217–22852 | 5 [3] | [2] 4 | [insI1]–[yagL] | [insI1],insN,eyeA,ykfC,insH1,mmuP,mmuM,afuC,afuB,insB1,insA,insI1,insX,yagB,yagA,yagE,yagF,yagG,yagH,yagI,argF,ykgS,insB1,insA,yagJ,yagK,[yagL] |
| * | * | ÷ | CP009273 | 289292 | 299008 | 9717 | 4 [2] | [3] 4 | [yagL]–[yagU] | [yagL],yagM,yagN,intF,ptwF,yagP,ykgT,paoD,paoC,paoB,paoA,[yagU] |
| * | * | ÷ | CP009273 | 299019 | 331147 | 32129 | 4 [3] | [3] 4 | [yagU]–[yahD] | [yagU],ykgJ,ecpE,ecpD,ecpC,ecpB,ecpA,ecpR,ykgL,ykgO,ykgM,ykgR,ykgP,eaeH,insE1,insF1,ykgA,ykgQ,rclC,rclB,rclA,rclR,ykgE,ykgF,ykgG,ykgH,betA,betB,betI,betT,yahA,yahB,yahC,[yahD] |
| * | * | ÷ | CP009273 | 331174 | 356540 | 25367 | 4 [3] | [3] 4 | [yahD]–[cynX] | [yahD],yahE,yahF,yahG,yahI,yahJ,yahK,yahL,yahM,yahN,yahO,prpR,prpB,prpC,prpD,prpE,codB,codA,cynR,cynT,cynS,[cynX] |
| * | * | ÷ | CP009273 | 356582 | 359329 | 2748 | 4 [3] | [3] 4 | [cynX]–[lacZ] | [cynX],lacA,lacY,[lacZ] |
| * | * | ÷ | CP009273 | 359348 | 367099–365993 | 6646–7752 | 4 [3] | [3] 4 | [lacZ]–mhpC | [lacZ],lacI,mhpR,mhpA,mhpB,mhpC |
| * | * | ÷ | CP009273 | 401686 | 401727 | 42 | 5 [3] | [2] 4 | yaiI/aroL | UPF0178 family protein/shikimate kinase II |
| * | * | ÷ | CP009273 | 428514 | 428557 | 44 | 4 [3] | [3] 4 | nrdR | Nrd regulon repressor |
| * | * | ÷ | CP009273 | 647493 | 647624 | 132 | 4 [3] | [3] 4 | citC/citA | [citrate [pro‑3S]‑lyase] ligase/sensory histidine kinase in two‑component regulatory system with CitB |
| * | * | ÷ | CP009273 | 1207519 | 1207619 | 101 | 4 [3] | [3] 4 | iraM/ycgX | RpoS stabilzer during Mg starvation, anti‑RssB factor/DUF1398 family protein |
| * | * | ÷ | CP009273 | 1209566 | 1209714 | 149 | 4 [3] | [3] 4 | bluR/bluF | repressor of blue light‑responsive genes/anti‑repressor for YcgE, blue light‑responsive; FAD‑binding; has c‑di‑GMP phosphodiesterase‑like EAL domain, but does not degrade c‑di‑GMP |
| * | * | ÷ | CP009273 | 1610345 | 1610436 | 92 | 4 [3] | [3] 4 | yneK | uncharacterized protein |
| * | * | ÷ | CP009273 | 1631396 | 1631467 | 72 | 4 [3] | [3] 5 | ydfO | Qin prophage; uncharacterized protein |
| * | * | ÷ | CP009273 | 2050181 | 2050288 | 108 | 4 [3] | [2] 4 | amn/yeeN | AMP nucleosidase/UPF0082 family protein |
| * | * | ÷ | CP009273 | 2051096 | 2051141 | 46 | 5 [3] | [3] 4 | yeeN/asnW | UPF0082 family protein/tRNA‑Asn |
| * | * | ÷ | CP009273 | 2099614 | 2099689 | 76 | 4 [3] | [3] 4 | wbbH | O‑antigen polymerase |
| * | * | ÷ | CP009273 | 2185809 | 2185910 | 102 | 4 [3] | [3] 4 | yehD/yehE | putative fimbrial‑like adhesin protein/DUF2574 family protein |
| * | * | ÷ | CP009273 | 2359177 | 2359295 | 119 | 4 [2] | [3] 4 | ais/arnB | putative LPS core heptose(II)‑phosphate phosphatase/uridine 5'‑(beta‑1‑threo‑pentapyranosyl‑4‑ulose diphosphate) aminotransferase, PLP‑dependent |
| * | * | ÷ | CP009273 | 2449485 | 2449510 | 26 | 4 [3] | [2] 4 | yfcV/sixA | putative fimbrial‑like adhesin protein/phosphohistidine phosphatase |
| * | * | ÷ | CP009273 | 2462761 | 2462958 | 198 | 4 [2] | [3] 4 | gtrS | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| * | * | ÷ | CP009273 | 2463175 | 2463237 | 63 | 4 [3] | [3] 4 | gtrS | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| * | * | ÷ | CP009273 | 2463562 | 2463725 | 164 | 4 [3] | [3] 4 | gtrS | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| * | * | ÷ | CP009273 | 2569315 | 2569352 | 38 | 4 [2] | [2] 4 | eutS/maeB | putative ethanol utilization carboxysome structural protein/malic enzyme: putative oxidoreductase/putative phosphotransacetylase |
| * | * | ÷ | CP009273 | 2622968 | 2623082 | 115 | 4 [3] | [3] 4 | yfgG/yfgH | uncharacterized protein/outer membrane integrity lipoprotein |
| * | * | ÷ | CP009273 | 2735066 | 2735152 | 87 | 4 [2] | [3] 4 | [yfiL] | [yfiL] |
| * | * | ÷ | CP009273 | 2767051 | 2767077 | 27 | 5 [3] | [2] 5 | yfjW | CP4‑57 prophage; putative inner membrane protein |
| * | * | ÷ | CP009273 | 2779509 | 2779554 | 46 | 4 [3] | [2] 4 | ileY/ygaQ | tRNA‑Ile/uncharacterized protein; putative enzyme |
| * | * | ÷ | CP009273 | 2899056 | 2899087 | 32 | 4 [3] | [2] 6 | [yqcG]–[ygcG] | [yqcG],[ygcG] |
| * | * | ÷ | CP009273 | 2984411 | 2984474 | 64 | 4 [3] | [3] 4 | ygeF/ygeG | pseudogene/SycD‑like chaperone family TPR‑repeat‑containing protein |
| * | * | ÷ | CP009273 | 2985224 | 2985261 | 38 | 4 [0] | [2] 4 | ygeG/ygeH | SycD‑like chaperone family TPR‑repeat‑containing protein/putative transcriptional regulator |
| * | * | ÷ | CP009273 | 2988447 | 2988646 | 200 | 5 [3] | [3] 4 | [ygeK] | [ygeK] |
| * | * | ÷ | CP009273 | 3260567 | 3260585 | 19 | 4 [3] | [3] 4 | tdcA/tdcR | tdc operon transcriptional activator/L‑threonine dehydratase operon activator protein |
| * | * | ÷ | CP009273 | 3790615 | 3790657 | 43 | 4 [3] | [3] 4 | waaL | O‑antigen ligase |
| * | * | ÷ | CP009273 | 3791549 | 3791583 | 35 | 4 [3] | [3] 4 | [waaL] | [waaL] |
| * | * | ÷ | CP009273 | 3794412 | 3794472 | 61 | 4 [3] | [3] 4 | waaJ | UDP‑D‑glucose:(galactosyl)lipopolysaccharide glucosyltransferase |
| * | * | ÷ | CP009273 | 3798316 | 3798458 | 143 | 4 [3] | [3] 4 | waaS | lipopolysaccharide core biosynthesis protein |
| * | * | ÷ | CP009273 | 4241480 | 4241501 | 22 | 4 [2] | [2] 4 | yjbI | pseudogene, SopA‑related, pentapeptide repeats‑containing |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 1203246 = | 0 (0.000) | 30 (1.140) | 23/246 | NT | 100% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 0 (0.000) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 0 (0.000) | 25 (0.950) | 21/246 | NT | 100% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 0 (0.000) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 4618838 | 47 (1.580) | 3 (0.110) | 3/262 | NT | 6.6% | coding (1502/1668 nt) | yjjK | putative transporter subunit of ABC superfamily: ATP‑binding component |
| ? | CP009273 | = 4618924 | 41 (1.460) | coding (1416/1668 nt) | yjjK | putative transporter subunit of ABC superfamily: ATP‑binding component | |||||