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 | 18,124 | C→G | 33.5% | G212G (GGC→GGG) | nhaA → | Na(+):H(+) antiporter NhaA |
| RA | 18,144 | T→G | 25.3% | V219G (GTG→GGG) | nhaA → | Na(+):H(+) antiporter NhaA |
| RA | 170,227 | C→T | 8.3% | G150G (GGC→GGT) | fhuC → | iron(III) hydroxamate ABC transporter ATP binding subunit |
| RA | 237,112 | C→T | 8.7% | intergenic (+105/‑223) | aspV → / → yafT | tRNA‑Asp/lipoprotein YafT |
| RA | 238,497 | G→T | 19.3% | I80I (ATC→ATA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,523 | G→T | 29.2% | L72I (CTT→ATT) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,535 | G→T | 28.6% | H68N (CAT→AAT) | ykfM ← | uncharacterized protein YkfM |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 383,949 | A→G | 6.1% | intergenic (‑14/‑11) | yaiP ← / → ykiC | putative glucosyltransferase/protein YkiC |
| RA | 454,924 | G→T | 49.4% | intergenic (+135/‑209) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 508,447 | T→G | 24.3% | V77G (GTT→GGT) | ybaQ → | putative DNA‑binding transcriptional regulator YbaQ |
| RA | 703,783 | C→T | 7.7% | intergenic (‑172/‑161) | nagB ← / → nagE | glucosamine‑6‑phosphate deaminase/N‑acetylglucosamine specific PTS enzyme IIABC component |
| RA | 806,415 | A→G | 5.8% | G289G (GGT→GGC) | ybhC ← | outer membrane lipoprotein YhbC |
| RA | 910,801 | G→A | 7.1% | N83N (AAC→AAT) | poxB ← | pyruvate oxidase |
| RA | 967,766 | A→G | 6.1% | K382K (AAA→AAG) | msbA → | ATP‑binding lipopolysaccharide transport protein |
| RA | 1,032,136 | G→A | 5.9% | intergenic (‑424/‑3) | serT ← / → hyaA | tRNA‑Ser/hydrogenase 1 small subunit |
| RA | 1,109,476 | C→G | 5.4% | P48A (CCC→GCC) | opgG → | osmoregulated periplasmic glucans (OPGs) biosynthesis protein G |
| RA | 1,136,652 | A→T | 6.1% | K127* (AAG→TAG) | flgI → | flagellar P‑ring protein |
| RA | 1,425,784 | C→G | 7.9% | A55G (GCT→GGT) | ydaY → | Rac prophage; putative uncharacterized protein YdaY |
| RA | 1,434,982 | C→A | 25.1% | pseudogene (27/51 nt) | ttcC ← | putative tRNA 2‑thiocytidine (s(2)C32) synthase |
| RA | 1,553,862 | T→A | 6.8% | intergenic (‑24/+110) | adhP ← / ← maeA | ethanol dehydrogenase/alcohol dehydrogenase/malate dehydrogenase, NAD‑requiring |
| RA | 1,599,849 | T→A | 6.2% | S121C (AGC→TGC) | lsrK ← | autoinducer‑2 kinase |
| RA | 1,642,447 | G→T | 12.0% | intergenic (+236/+42) | ynfS → / ← ydfT | Qin prophage; protein YnfS/Qin prophage; putative antitermination protein Q |
| RA | 1,660,118 | A→T | 6.5% | T684S (ACC→TCC) | ynfE → | putative selenate reductase YnfE |
| RA | 1,681,300 | C→A | 7.7% | H109N (CAC→AAC) | folM → | dihydromonapterin reductase |
| RA | 1,715,524 | A→T | 6.6% | C122* (TGT→TGA) | pdxY ← | pyridoxal kinase 2 |
| RA | 1,815,638 | A→G | 9.2% | Y591C (TAC→TGC) | katE → | catalase II |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,139,574 | A→C | 28.1% | intergenic (+89/+185) | yegH → / ← asmA | inner membrane protein YegH/putative assembly protein AsmA |
| RA | 2,139,598 | T→G | 35.7% | intergenic (+113/+161) | yegH → / ← asmA | inner membrane protein YegH/putative assembly protein AsmA |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,173,701 | A→G | 9.4% | pseudogene (578/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,177,234 | C→A | 55.3% | intergenic (‑30/+278) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,177,245 | G→T | 73.1% | intergenic (‑41/+267) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,239,670 | T→A | 5.3% | I227F (ATC→TTC) | mglB ← | D‑galactose/methyl‑galactoside ABC transporter periplasmic binding protein |
| RA | 2,310,839 | T→C | 20.7% | Q232Q (CAA→CAG) | ftp ← | FAD:protein FMN transferase |
| RA | 2,314,245 | A→C | 16.5% | D253A (GAC→GCC) | rcsD → | RcsD phosphotransferase |
| RA | 2,415,581 | A→T | 6.5% | T279S (ACT→TCT) | pta → | phosphate acetyltransferase |
| RA | 2,449,194 | A→C | 52.7% | intergenic (+37/+34) | smrB → / ← yfcO | putative endonuclease SmrB/DUF2544 domain‑containing protein YfcO |
| RA | 2,470,441 | C→A | 48.7% | D437E (GAC→GAA) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,470,463 | G→T | 40.7% | intergenic (+1/+614) | yfdI → / ← yfdK | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase/CPS‑53 (KpLE1) prophage; putative tail fiber assembly protein YfdK |
| RA | 2,540,731 | A→G | 9.9% | G28G (GGT→GGC) | cysA ← | sulfate/thiosulfate ABC transporter ATP binding subunit |
| RA | 2,601,038 | C→T | 6.9% | intergenic (+90/‑163) | bcp → / → hyfA | thiol peroxidase/hydrogenase 4 component A |
| RA | 2,647,305 | T→G | 20.4% | K7N (AAA→AAC) | pbpC ← | peptidoglycan glycosyltransferase PbpC |
| RA | 2,673,439 | G→T | 20.2% | G32C (GGT→TGT) | yphA → | putative inner membrane protein |
| RA | 2,763,411 | C→T | 7.6% | V44M (GTG→ATG) | abpB ← | CP4‑57 prophage; putative helicase YfjK |
| RA | 3,132,301 | A→C | 24.7% | G36G (GGT→GGG) | yghQ ← | putative transport protein YghQ |
| RA | 3,224,480 | C→T | 7.6% | V616V (GTC→GTT) | ebgA → | evolved beta‑D‑galactosidase subunit alpha |
| RA | 3,229,190 | G→A | 6.8% | Q101Q (CAG→CAA) | ygjK → | glycoside hydrolase |
| RA | 3,323,645 | C→T | 5.7% | S142S (TCG→TCA) | glmM ← | phosphoglucosamine mutase |
| RA | 3,438,474 | T→A | 5.8% | N59I (AAT→ATT) | arfA ← | alternative ribosome‑rescue factor A |
| RA | 3,454,069 | G→T | 25.4% | Q444K (CAA→AAA) | gspA ← | Type II secretion system protein GspA |
| RA | 3,465,172 | C→G | 16.5% | L31V (CTT→GTT) | gspM → | Type II secretion system protein GspM |
| RA | 3,544,147 | G→A | 8.3% | A233V (GCG→GTG) | bioH ← | pimeloyl‑acyl carrier protein methyl ester esterase |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph] | [rph] | |
| RA | 3,828,980 | A→C | 47.9% | Q12H (CAA→CAC) | xanP → | xanthine:H(+) symporter XanP |
| RA | 3,893,725 | C→T | 6.5% | intergenic (+1/‑156) | yidZ → / → yieE | putative LysR‑type transcriptional regulator YidZ/putative phosphopantetheinyl transferase |
| RA | 3,974,317 | T→A | 8.8% | V237E (GTA→GAA) | rffH → | dTDP‑glucose pyrophosphorylase 2 |
| RA | 4,028,727 | G→A | 5.4% | R16C (CGT→TGT) | fadA ← | 3‑ketoacyl‑CoA thiolase |
| MC JC | 4,123,449 | Δ990 bp | 100% | coding (19‑1008/1026 nt) | cytR ← | DNA‑binding transcriptional repressor CytR |
| JC | 4,186,098 | +TCCGCTGGT | 100% | coding (749/4224 nt) | rpoC → | RNA polymerase subunit beta' |
| RA | 4,198,170 | C→T | 6.0% | A152V (GCG→GTG) | hemE → | uroporphyrinogen decarboxylase |
| RA | 4,283,228 | T→G | 34.3% | intergenic (‑153/+25) | yjcF ← / ← actP | pentapeptide repeat‑containing protein YjcF/acetate/glycolate:cation symporter |
| RA | 4,296,060 | C→T | 23.4% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,495,943 | A→T | 7.0% | I89I (ATT→ATA) | ahr ← | aldehyde reductase, NADPH‑dependent |
| RA | 4,503,182 | G→A | 5.8% | R84C (CGC→TGC) | insG ← | KpLE2 phage‑like element; IS4 putative transposase |
| RA | 4,621,606 | T→A | 7.0% | intergenic (+4/‑163) | deoD → / → yjjJ | purine nucleoside phosphorylase/toxin YjjJ |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423769–3424558 | 3424558 | 1–790 | 18 [14] | [13] 16 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 24 (0.470) | 33 (0.750) | 22/204 | NT | 61.8% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 20 (0.450) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 24 (0.470) | 20 (0.450) | 15/204 | NT | 49.5% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 20 (0.450) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 64 (1.300) | 36/228 | NT | 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 | |||||