mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | 238,497 | G→T | 28.1% | I80I (ATC→ATA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,503 | G→T | 22.5% | F78L (TTC→TTA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,535 | G→T | 26.9% | H68N (CAT→AAT) | ykfM ← | uncharacterized protein YkfM |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 454,873 | C→G | 39.1% | intergenic (+84/‑260) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 531,291 | A→G | 7.4% | intergenic (‑65/+4) | selU ← / ← allS | tRNA 2‑selenouridine synthase/DNA‑binding transcriptional activator AllS |
| JC | 549,626 | Δ5 bp | 6.2% | [ylbF] | [ylbF] | |
| RA | 550,949 | T→C | 8.5% | L171L (TTG→CTG) | ybcF → | putative carbamate kinase |
| RA | 561,614 | G→A | 7.5% | V640I (GTA→ATA) | sfmD → | putative fimbrial usher protein SfmD |
| RA | 573,032 | A→T | 5.4% | T38S (ACC→TCC) | ninE → | DLP12 prophage; NinE family prophage protein |
| RA | 609,461 | A→T | 6.4% | *207K (TAA→AAA) | entD ← | phosphopantetheinyl transferase EntD |
| RA | 773,350 | T→G | 24.3% | G103G (GGT→GGG) | cydB → | cytochrome bd‑I ubiquinol oxidase subunit II |
| RA | 803,096 | G→A | 7.1% | A404T (GCA→ACA) | ybhI → | putative tricarboxylate transporter |
| RA | 870,697 | G→T | 7.6% | W429C (TGG→TGT) | gsiB → | glutathione ABC transporter periplasmic binding protein |
| RA | 874,921 | A→G | 7.5% | K648R (AAG→AGG) | pdeI → | putative c‑di‑GMP phosphodiesterase PdeI |
| RA | 965,512 | T→A | 8.7% | V398E (GTG→GAG) | ycaI → | conserved inner membrane protein YcaI |
| RA | 974,032 | G→T | 19.5% | D166Y (GAT→TAT) | cmoM → | tRNA cmo(5)U34 methyltransferase |
| RA | 1,148,547 | T→C | 7.9% | N309N (AAT→AAC) | plsX → | putative phosphate acyltransferase |
| RA | 1,157,887 | G→T | 85.5% | A7S (GCT→TCT) | ptsG → | glucose‑specific PTS enzyme IIBC component |
| RA | 1,186,691 | A→G | 5.9% | D283G (GAC→GGC) | pepT → | peptidase T |
| RA | 1,283,054 | C→T | 7.3% | P1064L (CCG→CTG) | narG → | nitrate reductase A subunit alpha |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | insH21 | insH21 | |
| RA | 1,417,846 | C→A | 5.1% | E55* (GAA→TAA) | ydaE ← | Rac prophage; zinc‑binding protein |
| RA | 1,607,996 | T→C | 7.0% | F217F (TTT→TTC) | tam → | trans‑aconitate 2‑methyltransferase |
| RA | 1,708,930 | C→A | 17.6% | P671Q (CCG→CAG) | rsxC → | SoxR [2Fe‑2S] reducing system protein RsxC |
| JC JC | 1,802,670 | IS2 (–) +5 bp | 19.7% | intergenic (‑100/‑420) | thrS ← / → arpB | threonine‑‑tRNA ligase/putative ankyrin repeat protein B, N‑terminal fragment |
| RA | 1,870,708 | G→T | 14.8% | M108I (ATG→ATT) | cdgI → | putative c‑di‑GMP binding protein CdgI |
| RA | 1,940,244 | G→A | 9.2% | intergenic (‑51/+69) | lpxM ← / ← mepM | myristoyl‑acyl carrier protein‑dependent acyltransferase/peptidoglycan DD‑endopeptidase MepM |
| RA | 1,970,084 | T→G | 14.5% | T301P (ACG→CCG) | tap ← | methyl‑accepting chemotaxis protein Tap |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| 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 | 49.7% | intergenic (‑30/+278) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,177,245 | G→T | 47.1% | intergenic (‑41/+267) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,301,660 | T→G | 6.6% | K365T (AAA→ACA) | napA ← | periplasmic nitrate reductase subunit NapA |
| RA | 2,317,258 | A→G | 9.7% | L873L (CTT→CTC) | rcsC ← | sensory histidine kinase RcsC |
| RA | 2,400,065 | C→T | 6.5% | C34Y (TGC→TAC) | nuoG ← | NADH:quinone oxidoreductase subunit G |
| RA | 2,596,869 | C→T | 14.1% | intergenic (‑132/+36) | ypfJ ← / ← purC | uncharacterized protein YpfJ/phosphoribosylaminoimidazole‑succinocarboxamide synthase |
| RA | 2,721,222 | C→T | 6.3% | P424S (CCG→TCG) | patZ → | peptidyl‑lysine acetyltransferase |
| RA | 2,789,151 | C→T | 6.1% | A56V (GCG→GTG) | csiD → | PF08943 family protein CsiD |
| RA | 2,853,188 | G→C | 6.0% | A351A (GCG→GCC) | hypD → | Fe‑(CN)2CO cofactor assembly scaffold protein HypD |
| RA | 2,909,215 | A→T | 5.6% | L151* (TTG→TAG) | pyrG ← | CTP synthetase |
| RA | 2,924,069 | Δ1 bp | 5.3% | coding (45/330 nt) | yqcC ← | DUF446 domain‑containing protein YqcC |
| RA | 2,927,317 | A→G | 6.2% | K337R (AAA→AGA) | ppnN → | nucleotide 5'‑monophosphate nucleosidase |
| RA | 2,960,585 | T→C | 5.5% | Q615R (CAA→CGA) | recC ← | exodeoxyribonuclease V subunit RecC |
| RA | 3,171,103 | T→A | 20.4% | L207Q (CTA→CAA) | qseC → | sensory histidine kinase QseC |
| RA | 3,266,246 | C→T | 5.1% | A274T (GCC→ACC) | tdcA ← | DNA‑binding transcriptional activator TdcA |
| JC JC | 3,410,277 | IS1 (+) +9 bp | 83.5% | [dusB] | [dusB] | |
| RA | 3,418,500 | T→A | 28.5% | N37K (AAT→AAA) | yhdV → | lipoprotein YhdV |
| RA | 3,454,069 | G→T | 29.5% | Q444K (CAA→AAA) | gspA ← | Type II secretion system protein GspA |
| RA | 3,465,696 | C→T | 5.6% | H52Y (CAT→TAT) | gspO → | Type II secretion system prepilin peptidase |
| RA | 3,472,570 | C→T | 7.8% | E315E (GAG→GAA) | fusA ← | elongation factor G |
| RA | 3,485,247 | T→C | 8.1% | F253S (TTC→TCC) | prkB → | putative phosphoribulokinase |
| RA | 3,535,018 | A→C | 100% | F284C (TTT→TGT) | envZ ← | sensory histidine kinase EnvZ |
| RA | 3,536,534 | A→G | 5.1% | R17R (CGT→CGC) | ompR ← | DNA‑binding transcriptional dual regulator OmpR |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| JC JC | 3,725,815 | IS2 (–) +5 bp | 17.8% | intergenic (‑103/‑68) | ysaB ← / → wecH | putative lipoprotein YsaB/O‑acetyltransferase WecH |
| RA | 3,739,196 | G→A | 5.8% | R567H (CGC→CAC) | malS → | alpha‑amylase |
| RA | 3,831,738 | G→A | 8.3% | G428S (GGC→AGC) | yicH → | AsmA famly protein YicH |
| RA | 3,913,868 | G→C | 5.2% | Q445E (CAG→GAG) | glmU ← | fused N‑acetylglucosamine‑1‑phosphate uridyltransferase and glucosamine‑1‑phosphate acetyltransferase |
| RA | 3,919,202 | G→C | 6.6% | A219G (GCT→GGT) | atpA ← | ATP synthase F1 complex subunit alpha |
| RA | 3,949,541 | T→C | 7.7% | E143E (GAA→GAG) | yifB ← | putative magnesium chelatase YifB |
| RA | 3,979,607 | C→T | 5.8% | T336M (ACG→ATG) | wzyE → | enterobacterial common antigen polymerase |
| RA | 4,078,180 | Δ1 bp | 7.0% | coding (732/990 nt) | yiiD → | putative acetyltransferase YiiD |
| JC JC | 4,118,284 | IS5 (–) +4 bp | 31.4% | intergenic (‑194/‑228) | glpF ← / → zapB | glycerol facilitator/cell division factor ZapB |
| RA | 4,122,384 | C→T | 6.0% | G319D (GGT→GAT) | ftsN ← | cell division protein FtsN |
| RA | 4,139,507 | T→A | 24.6% | M68L (ATG→TTG) | fsaB ← | fructose‑6‑phosphate aldolase 2 |
| JC | 4,186,098 | +TCCGCTGGT | 30.5% | coding (749/4224 nt) | rpoC → | RNA polymerase subunit beta' |
| RA | 4,200,226 | C→A | 17.8% | intergenic (+132/‑55) | yjaG → / → hupA | conserved protein YjaG/DNA‑binding protein HU‑alpha |
| RA | 4,200,392 | G→T | 31.4% | E38* (GAA→TAA) | hupA → | DNA‑binding protein HU‑alpha |
| RA | 4,207,653 | C→T | 6.2% | intergenic (‑121/‑494) | purH ← / → rrsE | bifunctional AICAR transformylase/IMP cyclohydrolase/16S ribosomal RNA |
| RA | 4,244,604 | G→T | 20.9% | Q158K (CAA→AAA) | malF ← | maltose ABC transporter membrane subunit MalF |
| RA | 4,288,284 | G→A | 6.0% | G174D (GGC→GAC) | nrfA → | cytochrome c552 nitrite reductase |
| RA | 4,289,718 | A→G | 6.1% | G158G (GGA→GGG) | nrfB → | periplasmic nitrite reductase penta‑heme c‑type cytochrome |
| RA | 4,296,060 | C→T | 23.7% | 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 | 4,588,953 | T→C | 6.2% | S43G (AGC→GGC) | yjiX ← | conserved protein YjiX |
| RA | 4,592,476 | G→C | 7.6% | A274P (GCC→CCC) | tsr → | methyl‑accepting chemotaxis protein Tsr |
| RA | 4,617,739 | Δ1 bp | 7.7% | coding (417/780 nt) | deoC → | deoxyribose‑phosphate aldolase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423780–3424234 | 3424546–3424239 | 6–767 | 16 [15] | [14] 17 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3486117 | 3486785 | 669 | 17 [15] | [14] 21 | crp | crp |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 5 (0.090) | 60 (1.310) | 38/204 | NT | 92.1% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 6 (0.130) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 5 (0.090) | 32 (0.700) | 25/204 | NT | 86.1% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 6 (0.130) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 1467910 = | NA (NA) | 5 (0.090) | 5/236 | NT | NA | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 1469242 | NA (NA) | intergenic (‑93/‑4) | insC‑2/ydbA | IS2 insertion element repressor InsA/putative outer membrane protein, N‑terminal fragment | |||||
| * | ? | NC_000913 | 2068941 = | NA (NA) | 3 (0.060) | 3/236 | NT | NA | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 2070273 | NA (NA) | intergenic (‑93/‑4) | insC‑3/yoeA | CP4‑44 prophage; IS2 insertion element repressor InsA/CP4‑44 prophage; TonB‑dependent receptor plug domain‑containing protein YoeA | |||||