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 | seq id | position | mutation | annotation | gene | description |
| RA | BN000925 | 9,791 | A→G | D797G (GAC→GGC) | tnpA → | Tn1 transposase |
| RA | BN000925 | 9,802 | G→A | D801N (GAC→AAC) | tnpA → | Tn1 transposase |
| RA | BN000925 | 10,089 | A→C | A896A (GCA→GCC) | tnpA → | Tn1 transposase |
| RA | BN000925 | 10,359 | T→A | G986G (GGT→GGA) | tnpA → | Tn1 transposase |
| RA | BN000925 | 12,239 | +A | intergenic (‑601/+1055) | klcA ← / ← tetR | KlcA putative anti‑restriction protein/tetracycline resistance repressor protein |
| RA | BN000925 | 12,406 | T→G | intergenic (‑768/+888) | klcA ← / ← tetR | KlcA putative anti‑restriction protein/tetracycline resistance repressor protein |
| RA | BN000925 | 12,688 | T→A | intergenic (‑1050/+606) | klcA ← / ← tetR | KlcA putative anti‑restriction protein/tetracycline resistance repressor protein |
| RA | BN000925 | 14,294 | G→C | G82A (GGC→GCC) | tetA → | tetracycline exporter protein |
| RA | BN000925 | 14,702 | T→C | V218A (GTC→GCC) | tetA → | tetracycline exporter protein |
| RA | BN000925 | 15,561 | Δ1 bp | intergenic (+312/+320) | tetA → / ← upf16.5 | tetracycline exporter protein/hypothetical protein |
| RA | BN000925 | 15,639 | C→G | intergenic (+390/+242) | tetA → / ← upf16.5 | tetracycline exporter protein/hypothetical protein |
| RA | BN000925 | 15,898 | +C | coding (649/666 nt) | upf16.5 ← | hypothetical protein |
| RA | BN000925 | 16,410 | +T | coding (137/666 nt) | upf16.5 ← | hypothetical protein |
| RA | BN000925 | 31,028 | C→G | P35A (CCC→GCC) | trbP → | TrbP protein |
| RA | BN000925 | 36,655 | A→G | R116G (AGA→GGA) R108G (AGA→GGA) |
istA → istA → |
IS21 transposase IS21 transposase |
| RA | BN000925 | 38,388 | A→C | pseudogene (45/171 nt) | upf35.8 → | probable truncation of theoretical product due to sequence errors |
| RA | BN000925 | 38,390 | 1 bp→AG | pseudogene (47/171 nt) | upf35.8 → | probable truncation of theoretical product due to sequence errors |
| RA | BN000925 | 38,393 | C→T | pseudogene (50/171 nt) | upf35.8 → | probable truncation of theoretical product due to sequence errors |
| RA | BN000925 | 38,421 | Δ1 bp | pseudogene (78/171 nt) | upf35.8 → | probable truncation of theoretical product due to sequence errors |
| RA | BN000925 | 38,510 | Δ1 bp | pseudogene (167/171 nt) | upf35.8 → | probable truncation of theoretical product due to sequence errors |
| RA | BN000925 | 38,526 | Δ1 bp | intergenic (+12/‑232) | upf35.8 → / → aphA | probable truncation of theoretical product due to sequence errors/aminoglycoside 3'‑phospho‑transferase |
| RA | BN000925 | 39,136 | Δ1 bp | coding (379/774 nt) | aphA → | aminoglycoside 3'‑phospho‑transferase |
| RA | BN000925 | 39,147 | Δ1 bp | coding (390/774 nt) | aphA → | aminoglycoside 3'‑phospho‑transferase |
| RA | BN000925 | 39,179 | +CG | coding (422/774 nt) | aphA → | aminoglycoside 3'‑phospho‑transferase |
| RA | BN000925 | 53,069 | +T | intergenic (+42/+10) | traM → / ← kfrC | TraM protein/KfrC protein |
| RA | BN000925 | 54,833 | Δ1 bp | intergenic (‑32/+127) | kfrB ← / ← kfrA | KfrB protein/KfrA coiled‑coil protein |
| RA | BN000925 | 56,817 | Δ1 bp | coding (297/522 nt) | korF ← | KorF repressor protein |
| RA | NC_000913 | 279 | (A)6→5 | intergenic (+24/‑58) | thrL → / → thrA | thr operon leader peptide/fused aspartate kinase/homoserine dehydrogenase 1 |
| RA | NC_000913 | 11,817 | (G)5→6 | intergenic (‑31/‑346) | yaaI ← / → dnaK | DUF2541 domain‑containing protein YaaI/chaperone protein DnaK |
| RA | NC_000913 | 18,216 | A→C | H243P (CAT→CCT) | nhaA → | Na(+):H(+) antiporter NhaA |
| RA | NC_000913 | 56,760 | A→G | V117A (GTG→GCG) | lptD ← | lipopolysaccharide assembly protein LptD |
| RA | NC_000913 | 77,593 | (T)8→7 | noncoding (227/227 nt) | sgrS → | small regulatory RNA SgrS |
| RA | NC_000913 | 137,824 | A→G | T248A (ACC→GCC) | cueO → | cuprous oxidase/multicopper oxidase with role in copper homeostasis |
| RA | NC_000913 | 169,409 | G→A | V642V (GTG→GTA) | fhuA → | ferrichrome outer membrane transporter/phage receptor |
| MC JC | NC_000913 | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | NC_000913 | 370,943 | T→C | F223L (TTT→CTT) | mhpB → | 3‑carboxyethylcatechol 2,3‑dioxygenase |
| RA | NC_000913 | 380,022 | (G)10→11 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | NC_000913 | 395,741 | A→G | Y183H (TAC→CAC) | ampH ← | peptidoglycan DD‑carboxypeptidase/peptidoglycan DD‑endopeptidase |
| RA | NC_000913 | 446,575 | A→G | V31A (GTT→GCT) | yajR ← | putative major facilitator superfamily transport protein YajR |
| RA | NC_000913 | 485,773 | A→G | T5A (ACC→GCC) | acrR → | DNA‑binding transcriptional repressor AcrR |
| RA | NC_000913 | 560,944 | Δ1 bp | coding (1248/2604 nt) | sfmD → | putative fimbrial usher protein SfmD |
| RA | NC_000913 | 561,696 | (G)6→5 | coding (2000/2604 nt) | sfmD → | putative fimbrial usher protein SfmD |
| RA | NC_000913 | 690,601 | A→G | V94A (GTG→GCG) | lnt ← | apolipoprotein N‑acyltransferase |
| RA | NC_000913 | 726,592 | (C)5→6 | coding (445/2049 nt) | kdpB ← | K(+) transporting P‑type ATPase subunit KdpB |
| RA | NC_000913 | 768,936 | A→G | Y320C (TAC→TGC) | mngB → | alpha‑mannosidase |
| RA | NC_000913 | 827,384 | T→C | Y533C (TAC→TGC) | ybhF ← | putative ABC exporter ATP binding subunit |
| RA | NC_000913 | 927,004 | A→G | G143G (GGT→GGC) | aat ← | leucyl/phenylalanyl‑tRNA‑‑protein transferase |
| RA | NC_000913 | 981,850 | (G)6→5 | coding (804/1848 nt) | ldtD → | L,D‑transpeptidase LdtD |
| RA | NC_000913 | 986,785 | Δ1 bp | coding (198/1089 nt) | ompF ← | outer membrane porin F |
| RA | NC_000913 | 1,001,023 | (A)8→7 | coding (1808/2601 nt) | elfC → | putative fimbrial usher protein ElfC |
| RA | NC_000913 | 1,001,379 | A→G | T722A (ACC→GCC) | elfC → | putative fimbrial usher protein ElfC |
| RA | NC_000913 | 1,012,027 | G→A | K9K (AAG→AAA) | pqiA → | intermembrane transport protein PqiA |
| RA | NC_000913 | 1,131,655 | Δ1 bp | coding (218/405 nt) | flgC → | flagellar basal‑body rod protein FlgC |
| RA | NC_000913 | 1,165,718 | A→G | intergenic (+33/‑367) | ycfP → / → ndh | UPF0227 protein YcfP/NADH:quinone oxidoreductase II |
| RA | NC_000913 | 1,214,924 | C→T | S184S (TCG→TCA) | bluF ← | blue light‑responsive regulator of BluR |
| RA | NC_000913 | 1,258,968 | G→A | G60S (GGT→AGT) | ychH → | stress‑induced protein |
| RA | NC_000913 | 1,295,013 | C→T | pseudogene (310/897 nt) | insZ ← | putative transposase InsZ |
| RA | NC_000913 | 1,296,375 | A→G | F583L (TTC→CTC) | adhE ← | aldehyde‑alcohol dehydrogenase |
| MC JC | NC_000913 | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | NC_000913 | 1,350,022 | A→G | V29A (GTC→GCC) | yciW ← | putative oxidoreductase |
| RA | NC_000913 | 1,370,044 | (T)9→8 | intergenic (+41/‑172) | pspE → / → ycjM | thiosulfate sulfurtransferase PspE/glucosylglycerate phosphorylase |
| RA | NC_000913 | 1,408,346 | A→G | E99E (GAA→GAG) | zntB → | Zn(2(+)):H(+) symporter |
| RA | NC_000913 | 1,501,112 | A→G | E180E (GAA→GAG) | tehA → | tellurite resistance protein |
| RA | NC_000913 | 1,543,164 | A→G | G299G (GGT→GGC) | narU ← | nitrate/nitrite transporter NarU |
| RA | NC_000913 | 1,638,221 | A→G | G11G (GGT→GGC) | ynfR ← | Qin prophage; protein YnfR |
| RA | NC_000913 | 1,644,875 | T→A | I10F (ATT→TTT) | rem ← | Qin prophage; protein Rem |
| RA | NC_000913 | 1,658,974 | A→G | Q302Q (CAA→CAG) | ynfE → | putative selenate reductase YnfE |
| RA | NC_000913 | 1,683,130 | T→C | S83S (AGT→AGC) | rstB → | sensory histidine kinase RstB |
| RA | NC_000913 | 1,738,922 | T→C | T293A (ACG→GCG) | ydhB ← | putative LysR family DNA‑binding transcriptional regulator YdhB |
| RA | NC_000913 | 1,739,660 | G→A | P47S (CCG→TCG) | ydhB ← | putative LysR family DNA‑binding transcriptional regulator YdhB |
| RA | NC_000913 | 1,818,938 | T→C | V170V (GTA→GTG) | chbR ← | DNA‑binding transcriptional dual regulator ChbR |
| RA | NC_000913 | 1,865,169 | (C)6→7 | coding (468/855 nt) | yeaE ← | methylglyoxal reductase YeaE |
| RA | NC_000913 | 1,953,402 | A→G | N234S (AAC→AGC) | cmoA → | carboxy‑S‑adenosyl‑L‑methionine synthase |
| RA | NC_000913 | 1,978,440 | (G)6→7 | intergenic (‑243/+78) | flhD ← / ← insB‑5 | DNA‑binding transcriptional dual regulator FlhD/IS1 protein InsB |
| RA | NC_000913 | 2,065,747 | (C)6→7 | coding (18/546 nt) | cobU ← | cobinamide‑P guanylyltransferase/cobinamide kinase |
| RA | NC_000913 | 2,115,900 | T→C | intergenic (‑4/+7) | wcaM ← / ← wcaL | putative colanic acid biosynthesis protein WcaM/putative colanic biosynthesis glycosyl transferase |
| RA | NC_000913 | 2,173,142 | T→C | pseudogene (1137/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | NC_000913 | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | NC_000913 | 2,249,587 | A→T | F11Y (TTT→TAT) | yeiE ← | putative LysR‑type transcriptional regulator YeiE |
| RA | NC_000913 | 2,262,108 | T→C | V86V (GTA→GTG) | fruK ← | 1‑phosphofructokinase |
| RA | NC_000913 | 2,406,477 | T→C | K55K (AAA→AAG) | lrhA ← | DNA‑binding transcriptional dual regulator LrhA |
| RA | NC_000913 | 2,423,373 | T→C | D56G (GAC→GGC) | rpnB ← | recombination‑promoting nuclease RpnB |
| RA | NC_000913 | 2,554,617 | G→A | A189V (GCG→GTG) | eutR ← | putative AraC‑type transcriptional regulator EutR |
| RA | NC_000913 | 2,570,488 | A→G | C422R (TGC→CGC) | eutE ← | putative aldehyde dehydrogenase, ethanolamine utilization protein |
| RA | NC_000913 | 2,636,169 | T→C | Q396Q (CAA→CAG) | der ← | 50S ribosomal subunit stability factor |
| RA | NC_000913 | 2,656,737 | A→G | intergenic (‑1/+11) | iscX ← / ← fdx | accessory iron‑sulfur cluster assembly protein IscX/reduced ferredoxin |
| RA | NC_000913 | 2,679,079 | A→G | S97P (TCT→CCT) | yphF ← | putative ABC transporter periplasmic binding protein YphF |
| RA | NC_000913 | 2,695,585 | (G)7→8 | intergenic (‑42/‑216) | purL ← / → mltF | phosphoribosylformylglycinamide synthetase/membrane‑bound lytic murein transglycosylase F |
| RA | NC_000913 | 2,722,910 | G→A | D62N (GAC→AAC) | pssA → | phosphatidylserine synthase |
| RA | NC_000913 | 2,812,802 | G→A | A63T (GCC→ACC) | emrB → | multidrug efflux pump membrane subunit EmrB |
| RA | NC_000913 | 2,836,975 | T→C | T151A (ACC→GCC) | hypF ← | carbamoyltransferase HypF |
| RA | NC_000913 | 2,922,893 | T→C | H31R (CAC→CGC) | yqcA ← | putative flavodoxin YqcA |
| RA | NC_000913 | 2,930,244 | T→G | G223G (GGT→GGG) | sdaB → | L‑serine deaminase II |
| RA | NC_000913 | 2,963,642 | (C)5→4 | coding (75/564 nt) | ppdB ← | conserved protein PpdB |
| RA | NC_000913 | 2,987,636 | A→G | N34S (AAC→AGC) | yqeH → | putative LuxR family transcriptional regulator YqeH |
| RA | NC_000913 | 3,064,257 | A→G | T89A (ACC→GCC) | scpB → | methylmalonyl‑CoA decarboxylase |
| RA | NC_000913 | 3,084,099 | T→C | T605A (ACC→GCC) | speA ← | arginine decarboxylase, biosynthetic |
| RA | NC_000913 | 3,101,039 | (C)7→8 | coding (585/720 nt) | yggN ← | putative EcfF |
| RA | NC_000913 | 3,153,666 | C→T | T35M (ACG→ATG) | yghB → | DedA family protein YghB |
| RA | NC_000913 | 3,157,712 | (C)6→7 | coding (63/927 nt) | yqhG → | DUF3828 domain‑containing protein YqhG |
| RA | NC_000913 | 3,171,736 | G→A | G418E (GGG→GAG) | qseC → | sensory histidine kinase QseC |
| RA | NC_000913 | 3,360,538 | T→C | R447R (CGT→CGC) | gltD → | glutamate synthase subunit GltD |
| MC JC | NC_000913 | 3,366,751 | Δ295 bp | IS5‑mediated | yhcE–[yhcF] | yhcE, [yhcF] |
| RA | NC_000913 | 3,384,304 | G→A | intergenic (‑36/‑399) | mdh ← / → argR | malate dehydrogenase/DNA‑binding transcriptional dual regulator ArgR |
| RA | NC_000913 | 3,406,578 | A→G | N221S (AAC→AGC) | accC → | biotin carboxylase |
| RA | NC_000913 | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | NC_000913 | 3,717,751 | C→T | L148L (CTG→TTG) | ghrB → | glyoxylate reductase |
| RA | NC_000913 | 3,720,780 | T→C | V34A (GTC→GCC) | insJ → | insertion element IS150 protein InsA |
| RA | NC_000913 | 3,728,118 | (C)8→7 | coding (1254/1455 nt) | xylB ← | xylulokinase |
| RA | NC_000913 | 3,824,676 | T→C | G54G (GGT→GGC) | trmH → | tRNA (Gm18) 2'‑O‑methyltransferase |
| RA | NC_000913 | 3,902,990 | G→A | P238S (CCA→TCA) | bglB ← | 6‑phospho‑beta‑glucosidase B |
| RA | NC_000913 | 3,966,398 | T→C | intergenic (+66/‑19) | rhoL → / → rho | rho operon leader peptide/transcription termination factor Rho |
| RA | NC_000913 | 3,982,684 | (C)8→9 | noncoding (79/87 nt) | leuT → | tRNA‑Leu |
| RA | NC_000913 | 4,040,436 | G→C | intergenic (+13/‑81) | rrlA → / → rrfA | 23S ribosomal RNA/5S ribosomal RNA |
| RA | NC_000913 | 4,098,826 | A→G | T61A (ACC→GCC) | rhaR → | DNA‑binding transcriptional activator RhaR |
| RA | NC_000913 | 4,184,076 | T→C | R944R (CGT→CGC) | rpoB → | RNA polymerase subunit beta |
| RA | NC_000913 | 4,193,379 | G→A | S66S (AGC→AGT) | thiF ← | ThiS adenylyltransferase |
| RA | NC_000913 | 4,223,778 | T→C | intergenic (‑150/‑50) | iclR ← / → metH | DNA‑binding transcriptional repressor IclR/cobalamin‑dependent methionine synthase |
| RA | NC_000913 | 4,238,230 | T→C | G199G (GGT→GGC) | yjbH → | YjbH family protein |
| RA | NC_000913 | 4,256,567 | A→G | intergenic (‑101/‑70) | plsB ← / → dgkA | glycerol‑3‑phosphate 1‑O‑acyltransferase/diacylglycerol kinase |
| RA | NC_000913 | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | NC_000913 | 4,330,676 | (G)5→6 | coding (175/1503 nt) | proP → | osmolyte:H(+) symporter ProP |
| RA | NC_000913 | 4,340,918 | T→C | K237K (AAA→AAG) | melR ← | DNA‑binding transcriptional dual regulator MelR |
| RA | NC_000913 | 4,373,382 | C→T | A285T (GCA→ACA) | yjeJ ← | protein YjeJ |
| JC | NC_000913 | 4,397,624 | (GCTGGC)3→2 | coding (213‑218/1848 nt) | mutL → | DNA mismatch repair protein MutL |
| RA | NC_000913 | 4,497,694 | T→C | pseudogene (945/1191 nt) | intB → | KpLE2 phage‑like element; putative integrase |
| RA | NC_000913 | 4,517,951 | (C)6→7 | coding (285/522 nt) | fecI ← | RNA polymerase sigma factor FecI |
| RA | NC_000913 | 4,562,168 | T→C | T170A (ACG→GCG) | yjiJ ← | putative transporter YjiJ |
| RA | NC_000913 | 4,573,409 | A→G | R332R (AGA→AGG) | yjiT → | putative uncharacterized protein YjiT |
| RA | NC_000913 | 4,606,330 | (G)8→9 | noncoding (72/87 nt) | leuQ ← | tRNA‑Leu |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423876–3424233 | 3424463–3424238 | 6–588 | 16 [15] | [15] 17 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 807336 | 0 (0.000) | 38 (0.610) +G |
24/428 | 1.5 | 58.1% | intergenic (‑55/+97) | ybhC/ybhB | outer membrane lipoprotein YhbC/putative kinase inhibitor |
| ? | NC_000913 | = 4171849 | 55 (0.880) | intergenic (+93/‑208) | rrfB/murB | 5S ribosomal RNA/UDP‑N‑acetylenolpyruvoylglucosamine reductase | |||||
| * | ? | NC_000913 | 1207790 = | 75 (1.200) | 18 (0.310) | 14/398 | 2.6 | 21.8% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 60 (1.040) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 1550109 = | 54 (0.860) | 2504 (40.220) | 285/428 | 0.0 | 97.5% | coding (2709/3048 nt) | fdnG | formate dehydrogenase N subunit alpha |
| ? | NC_000913 | = 1553994 | 76 (1.220) | coding (1676/1698 nt) | maeA | malate dehydrogenase, NAD‑requiring | |||||