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 | 18,109 | C→G | 20.1% | V207V (GTC→GTG) | nhaA → | Na(+):H(+) antiporter NhaA |
| RA | 28,557 | G→A | 5.2% | V62M (GTG→ATG) | dapB → | 4‑hydroxy‑tetrahydrodipicolinate reductase |
| RA | 31,727 | T→G | 21.5% | V304G (GTG→GGG) | carB → | carbamoyl phosphate synthetase subunit beta |
| RA | 50,123 | G→T | 33.0% | E101* (GAA→TAA) | folA → | dihydrofolate reductase |
| RA | 72,017 | T→G | 22.2% | L223V (TTG→GTG) | yabI → | DedA family protein YabI |
| RA | 123,466 | T→G | 30.0% | A150A (GCT→GCG) | aceE → | pyruvate dehydrogenase E1 component |
| RA | 127,639 | A→T | 16.7% | intergenic (+52/‑273) | aceF → / → lpd | pyruvate dehydrogenase, E2 subunit/lipoamide dehydrogenase |
| RA | 171,602 | C→T | 7.5% | D47D (GAC→GAT) | fhuB → | iron(III) hydroxamate ABC transporter membrane subunit |
| RA | 202,743 | A→T | 5.0% | I62F (ATT→TTT) | lpxA → | UDP‑N‑acetylglucosamine acyltransferase |
| RA | 238,532 | C→A | 25.7% | V69L (GTA→TTA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,535 | G→T | 34.9% | H68N (CAT→AAT) | ykfM ← | uncharacterized protein YkfM |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 298,557 | A→C | 29.4% | L57R (CTC→CGC) | paoD ← | molybdenum cofactor insertion chaperone for PaoABC |
| RA | 322,569 | A→C | 9.5% | T78P (ACG→CCG) | ykgF → | putative amino acid dehydrogenase with NAD(P)‑binding domain and ferridoxin‑like domain |
| RA | 353,047 | T→C | 6.8% | Y114Y (TAT→TAC) | prpE → | propionyl‑CoA synthetase |
| RA | 353,470 | C→T | 8.0% | G255G (GGC→GGT) | prpE → | propionyl‑CoA synthetase |
| RA | 454,873 | C→G | 31.6% | intergenic (+84/‑260) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 454,877 | A→T | 40.9% | intergenic (+88/‑256) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 454,885 | C→G | 26.1% | intergenic (+96/‑248) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 454,924 | G→T | 34.3% | intergenic (+135/‑209) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 488,818 | T→G | 20.2% | R761R (CGT→CGG) | mscK → | potassium dependent, small conductance mechanosensitive channel |
| RA | 590,074 | G→A | 6.2% | S294F (TCT→TTT) | nfrA ← | bacteriophage N4 receptor, outer membrane protein |
| RA | 705,901 | G→A | 6.6% | intergenic (+11/‑192) | nagE → / → glnS | N‑acetylglucosamine specific PTS enzyme IIABC component/glutamine‑‑tRNA ligase |
| RA | 729,372 | A→C | 39.3% | intergenic (+32/‑211) | ybfA → / → rhsC | DUF2517 domain‑containing protein YbfA/rhs element protein RhsC |
| RA | 729,383 | T→G | 33.5% | intergenic (+43/‑200) | ybfA → / → rhsC | DUF2517 domain‑containing protein YbfA/rhs element protein RhsC |
| RA | 744,446 | G→A | 7.7% | G68G (GGG→GGA) | pxpC → | 5‑oxoprolinase component C |
| RA | 1,008,930 | T→A | 13.8% | Y363N (TAC→AAC) | rlmL → | fused 23S rRNA m(2)G2445 methyltransferase and 23S rRNA m(7)G2069 methyltransferase |
| RA | 1,106,692 | T→C | 6.5% | L113P (CTG→CCG) | clsC → | cardiolipin synthase C |
| RA | 1,157,593 | C→T | 38.3% | intergenic (+19/‑276) | ycfH → / → ptsG | putative metal‑dependent hydrolase YcfH/glucose‑specific PTS enzyme IIBC component |
| RA | 1,157,763 | G→A | 62.0% | intergenic (+189/‑106) | ycfH → / → ptsG | putative metal‑dependent hydrolase YcfH/glucose‑specific PTS enzyme IIBC component |
| RA | 1,224,931 | T→G | 28.6% | N144T (AAC→ACC) | minD ← | Z‑ring positioning protein MinD |
| RA | 1,235,630 | G→T | 7.5% | P231P (CCG→CCT) | fadR → | DNA‑binding transcriptional dual regulator FadR |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | insH21 | insH21 | |
| RA | 1,420,020 | G→T | 5.6% | N74K (AAC→AAA) | racR ← | Rac prophage; DNA‑binding transcriptional repressor RacR |
| RA | 1,482,157 | A→T | 6.1% | T417S (ACA→TCA) | ynbD → | putative phosphatase |
| RA | 1,605,272 | A→T | 5.9% | V74V (GTA→GTT) | lsrB → | Autoinducer‑2 ABC transporter periplasmic binding protein |
| RA | 1,630,756 | C→G | 5.2% | G53A (GGA→GCA) | ydfI ← | putative oxidoreductase YdfI |
| RA | 1,664,416 | C→G | 21.5% | L270V (CTC→GTC) | ynfH → | putative menaquinol dehydrogenase |
| RA | 1,675,421 | C→T | 9.5% | G314R (GGG→AGG) | pntB ← | pyridine nucleotide transhydrogenase subunit beta |
| RA | 1,708,930 | C→A | 15.7% | P671Q (CCG→CAG) | rsxC → | SoxR [2Fe‑2S] reducing system protein RsxC |
| RA | 1,770,263 | C→T | 6.8% | intergenic (+77/‑109) | ydiK → / → rprA | putative transporter YdiK/small regulatory RNA RprA |
| RA | 1,966,121 | C→A | 5.7% | G24V (GGG→GTG) | flhB ← | flagellar biosynthesis protein FlhB |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,139,584 | A→T | 23.8% | intergenic (+99/+175) | yegH → / ← asmA | inner membrane protein YegH/putative assembly protein AsmA |
| RA | 2,139,598 | T→G | 33.4% | intergenic (+113/+161) | yegH → / ← asmA | inner membrane protein YegH/putative assembly protein AsmA |
| RA | 2,140,054 | G→A | 5.6% | A520V (GCG→GTG) | asmA ← | putative assembly protein AsmA |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,177,234 | C→A | 53.6% | intergenic (‑30/+278) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,177,245 | G→T | 58.3% | intergenic (‑41/+267) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,339,597 | Δ1 bp | 5.1% | coding (31/723 nt) | ubiG → | bifunctional 3‑demethylubiquinone‑8 3‑O‑methyltransferase and 2‑octaprenyl‑6‑hydroxyphenol methylase |
| RA | 2,419,867 | C→T | 5.1% | A207T (GCA→ACA) | yfcF ← | glutathione S‑transferase YfcF |
| RA | 2,449,194 | A→C | 64.2% | intergenic (+37/+34) | smrB → / ← yfcO | putative endonuclease SmrB/DUF2544 domain‑containing protein YfcO |
| RA | 2,453,939 | T→A | 6.6% | pseudogene (1063/2646 nt) | yfcU ← | putative outer membrane usher protein YfcU |
| RA | 2,456,849 | C→A | 24.1% | intergenic (‑37/+166) | sixA ← / ← fadJ | phosphohistidine phosphatase/3‑hydroxyacyl‑CoA dehydrogenase FadJ |
| RA | 2,470,431 | G→T | 43.3% | R434I (AGA→ATA) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,470,435 | T→A | 31.7% | N435K (AAT→AAA) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,470,436 | C→A | 44.4% | Q436K (CAA→AAA) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,470,444 | T→A | 21.7% | N438K (AAT→AAA) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,470,463 | G→T | 44.3% | intergenic (+1/+614) | yfdI → / ← yfdK | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase/CPS‑53 (KpLE1) prophage; putative tail fiber assembly protein YfdK |
| RA | 2,518,276 | C→A | 21.7% | intergenic (‑45/‑191) | alaW ← / → yfeC | tRNA‑Ala/putative DNA‑binding transcriptional regulator YfeC |
| RA | 2,574,221 | G→A | 7.9% | R29C (CGC→TGC) | eutT ← | putative ethanolamine utilization cobalamin adenosyltransferase |
| RA | 2,662,551 | G→C | 15.3% | intergenic (‑420/+32) | iscR ← / ← trmJ | DNA‑binding transcriptional dual regulator IscR/tRNA Cm32/Um32 methyltransferase |
| RA | 2,673,429 | C→A | 20.6% | F28L (TTC→TTA) | yphA → | putative inner membrane protein |
| RA | 2,869,276 | T→C | 5.1% | I82V (ATT→GTT) | pcm ← | L‑isoaspartate protein carboxylmethyltransferase type II |
| RA | 3,029,108 | A→T | 5.3% | D608E (GAT→GAA) | ygfT ← | fused putative oxidoreductase, Fe‑S subunit and nucleotide‑binding subunit |
| RA | 3,031,440 | T→C | 5.2% | L25S (TTA→TCA) | uacT → | urate:H(+) symporter |
| RA | 3,121,249 | T→A | 5.6% | M11L (ATG→TTG) | glcA ← | glycolate/lactate:H(+) symporter GlcA |
| RA | 3,140,205 | G→C | 28.9% | C38W (TGC→TGG) | hybF ← | hydrogenase maturation protein HybF |
| RA | 3,264,802 | A→C | 17.1% | R72R (CGT→CGG) | tdcC ← | threonine/serine:H(+) symporter |
| RA | 3,331,815 | T→A | 6.0% | L307F (TTA→TTT) | yhbE ← | inner membrane protein YhbE |
| RA | 3,377,030 | G→A | 100% | Q131* (CAA→TAA) | sspA ← | stringent starvation protein A |
| RA | 3,408,007 | C→G | 25.5% | A134G (GCG→GGG) | panF → | pantothenate:Na(+) symporter |
| RA | 3,418,500 | T→A | 30.8% | N37K (AAT→AAA) | yhdV → | lipoprotein YhdV |
| RA | 3,448,232 | T→A | 18.5% | intergenic (‑83/+82) | rplN ← / ← rpsQ | 50S ribosomal subunit protein L14/30S ribosomal subunit protein S17 |
| RA | 3,448,257 | G→T | 22.2% | intergenic (‑108/+57) | rplN ← / ← rpsQ | 50S ribosomal subunit protein L14/30S ribosomal subunit protein S17 |
| RA | 3,454,069 | G→T | 33.1% | Q444K (CAA→AAA) | gspA ← | Type II secretion system protein GspA |
| RA | 3,454,530 | A→T | 5.5% | M290K (ATG→AAG) | gspA ← | Type II secretion system protein GspA |
| RA | 3,480,474 | C→T | 7.5% | W45* (TGG→TAG) | kefB ← | K(+) : H(+) antiporter KefB |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,625,117 | T→A | 8.0% | L247H (CTT→CAT) | yhhI → | putative transposase |
| RA | 3,625,154 | A→G | 5.8% | K259K (AAA→AAG) | yhhI → | putative transposase |
| RA | 3,661,324 | G→A | 5.1% | R304Q (CGG→CAG) | mdtF → | multidrug efflux pump RND permease MdtF |
| RA | 3,731,428 | A→T | 7.4% | K100* (AAA→TAA) | xylF → | xylose ABC transporter periplasmic binding protein |
| RA | 3,773,290 | G→A | 6.6% | S337N (AGC→AAC) | mtlA → | mannitol‑specific PTS enzyme IICBA component |
| RA | 3,782,876 | A→C | 20.9% | R262R (CGT→CGG) | gpsA ← | glycerol‑3‑phosphate dehydrogenase |
| RA | 3,902,809 | C→A | 18.4% | S298I (AGT→ATT) | bglB ← | 6‑phospho‑beta‑glucosidase B |
| RA | 3,995,691 | G→A | 5.7% | A37T (GCA→ACA) | yigA → | conserved protein YigA |
| RA | 4,021,547 | T→G | 27.2% | V441G (GTC→GGC) | ubiB → | ubiquinone biosynthesis protein UbiB |
| RA | 4,072,686 | C→A | 17.4% | V296L (GTA→TTA) | yihU ← | 3‑sulfolactaldehyde reductase |
| JC JC | 4,118,284 | IS5 (–) +4 bp | 49.7% | intergenic (‑194/‑228) | glpF ← / → zapB | glycerol facilitator/cell division factor ZapB |
| RA | 4,122,025 | A→T | 5.4% | M88K (ATG→AAG) | hslV ← | peptidase component of the HslVU protease |
| RA | 4,220,018 | G→T | 25.4% | D475Y (GAT→TAT) | aceK → | isocitrate dehydrogenase kinase/phosphatase |
| RA | 4,254,503 | A→T | 5.4% | L655Q (CTG→CAG) | plsB ← | glycerol‑3‑phosphate 1‑O‑acyltransferase |
| RA | 4,283,228 | T→G | 46.6% | intergenic (‑153/+25) | yjcF ← / ← actP | pentapeptide repeat‑containing protein YjcF/acetate/glycolate:cation symporter |
| RA | 4,295,929 | T→C | 11.1% | intergenic (+135/+507) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,296,060 | C→T | 28.6% | 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 | 4,321,100 | T→G | 16.9% | S50R (AGC→CGC) | phnH ← | carbon‑phosphorus lyase core complex subunit PhnH |
| RA | 4,378,977 | T→A | 32.5% | intergenic (‑33/+30) | ampC ← / ← frdD | beta‑lactamase/fumarate reductase membrane protein FrdD |
| RA | 4,398,359 | T→G | 22.9% | R316R (CGT→CGG) | mutL → | DNA mismatch repair protein MutL |
| RA | 4,410,389 | T→A | 5.5% | I86N (ATC→AAC) | yjfI → | conserved protein YjfI |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423760–3424234 | 3424532–3424238 | 5–773 | 20 [19] | [18] 21 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3486119 | 3486783 | 665 | 20 [15] | [19] 22 | crp | crp |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 381258 = | NA (NA) | 6 (0.090) | 6/234 | NT | NA | pseudogene (3/417 nt) | yaiX | putative acyltransferase, N‑terminal fragment |
| ? | NC_000913 | = 382589 | NA (NA) | noncoding (1330/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 35 (0.520) | 33 (0.570) | 24/204 | NT | 51.5% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 32 (0.550) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 32 (0.470) | 34 (0.580) | 24/204 | NT | 53.3% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 32 (0.550) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 23 (0.340) | 19/234 | NT | 52.3% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3377657 = | 21 (0.310) | intergenic (‑237/+158) | sspA/rpsI | stringent starvation protein A/30S ribosomal subunit protein S9 | |||||