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 | 7,905 | A→C | 7.8% | Y19D (TAC→GAC) | yaaJ ← | putative transporter |
| RA | 118,828 | G→T | 9.1% | D84Y (GAT→TAT) | pdhR → | pyruvate dehydrogenase complex repressor; autorepressor |
| RA | 153,858 | T→G | 8.2% | N121T (AAT→ACT) | folK ← | 2‑amino‑4‑hydroxy‑6‑hydroxymethyldihyropteridine pyrophosphokinase |
| RA | 158,967 | C→A | 8.3% | H126N (CAT→AAT) | hrpB → | putative ATP‑dependent helicase |
| RA | 161,068 | A→C | 10.5% | intergenic (+47/‑149) | hrpB → / → mrcB | putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase |
| JC JC | 188,334 | IS2 (+) +16 bp | 12.8% | [pyrH] | [pyrH] | |
| JC | 216,968 | Δ3 bp | 10.7% | coding (446‑448/816 nt) | metQ ← | DL‑methionine transporter subunit |
| RA | 233,053 | A→C | 6.5% | D167A (GAT→GCT) | dnaQ → | DNA polymerase III epsilon subunit |
| RA | 306,510 | G→A | 5.2% | R180W (CGG→TGG) | ecpR ← | putative transcriptional regulator for the ecp operon |
| RA | 345,428 | T→C | 6.3% | intergenic (+145/‑295) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 351,447 | T→A | 11.2% | L272Q (CTG→CAG) | codB → | cytosine transporter |
| RA | 353,486 | A→T | 5.5% | intergenic (+321/+16) | codA → / ← cynR | cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor |
| RA | 360,752 | A→G | 100% | V331A (GTG→GCG) | lacI ← | DNA‑binding transcriptional repressor |
| JC | 361,139 | +GCCA | 66.8% | coding (605/1083 nt) | lacI ← | DNA‑binding transcriptional repressor |
| RA | 361,806 | G→A | 100% | intergenic (‑63/+14) | lacI ← / ← mhpR | DNA‑binding transcriptional repressor/mhp operon transcriptional activator |
| RA | 473,180 | T→A | 6.8% | K298N (AAA→AAT) | ylaB ← | putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase |
| RA | 505,336 | C→T | 5.0% | E500E (GAG→GAA) | copA ← | copper transporter |
| RA | 513,720 | T→C | 6.2% | I6V (ATT→GTT) | ybbN ← | DnaK co‑chaperone, thioredoxin‑like protein |
| RA | 838,658 | G→T | 7.8% | A291S (GCC→TCC) | rlmF → | 23S rRNA m(6)A1618 methyltransferase, SAM‑dependent |
| JC JC | 919,057 | IS5 (–) +4 bp | 58.7% | coding (338‑341/2277 nt) | clpA → | ATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity |
| RA | 971,532 | A→T | 5.8% | Q152L (CAG→CTG) | mukE → | chromosome condensin MukBEF, MukE localization factor |
| RA | 1,122,159 | G→T | 6.9% | A183S (GCG→TCG) | yceH → | UPF0502 family protein |
| RA | 1,129,182 | G→A | 5.9% | A385T (GCC→ACC) | flgE → | flagellar hook protein |
| JC | 1,191,242 | +GTGACTCT | 30.3% | coding (664/1251 nt) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,192,525 | C→T | 5.0% | S155N (AGC→AAC) | ymfD ← | e14 prophage; putative SAM‑dependent methyltransferase |
| RA | 1,211,142 | C→T | 9.3% | intergenic (‑211/‑103) | bluF ← / → ycgZ | anti‑repressor for YcgE, blue light‑responsive; FAD‑binding; has c‑di‑GMP phosphodiesterase‑like EAL domain, but does not degrade c‑di‑GMP/RcsB connector protein for regulation of biofilm and acid‑resistance |
| RA | 1,282,421 | A→T | 6.4% | intergenic (+439/+101) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,282,439 | A→T | 6.4% | intergenic (+457/+83) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,361,433 | G→T | 5.6% | P246Q (CCG→CAG) | pspF ← | psp operon transcriptional activator |
| RA | 1,368,566 | T→G | 7.6% | F74V (TTC→GTC) | ycjP → | inner membrane putative ABC superfamily sugar transporter permease |
| JC JC | 1,376,043 | IS5 (–) +4 bp | 44.8% | pseudogene (10‑13/126 nt) | ycjV → | pseudogene; putative ATP‑binding component of a transport system |
| RA | 1,513,440 | T→A | 7.3% | Y53N (TAT→AAT) | curA → | curcumin/dihydrocurcumin reductase, NADPH‑dependent |
| RA | 1,607,556 | A→C | 6.9% | intergenic (‑48/+16) | glsB ← / ← sad | glutaminase 2/succinate semialdehyde dehydrogenase, NAD(P)+‑dependent |
| RA | 1,628,207 | G→A | 42.4% | G110E (GGA→GAA) | pinQ → | Qin prophage; putative site‑specific recombinase |
| RA | 1,703,062 | T→A | 5.3% | R629R (CGT→CGA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,704,060 | A→T | 6.6% | Q221L (CAA→CTA) | rsxD → | SoxR iron‑sulfur cluster reduction factor component; putative membrane protein of electron transport complex |
| RA | 1,780,104 | C→A | 6.4% | A422A (GCG→GCT) | ppsA ← | phosphoenolpyruvate synthase |
| RA | 1,795,380 | A→T | 62.5% | V483E (GTA→GAA) | thrS ← | threonyl‑tRNA synthetase |
| RA | 1,824,998 | G→T | 6.6% | R9R (CGA→AGA) | astA ← | arginine succinyltransferase |
| RA | 1,884,059 | G→A | 5.3% | intergenic (‑56/+149) | fadD ← / ← yeaY | acyl‑CoA synthetase (long‑chain‑fatty‑acid‑‑CoA ligase)/Slp family lipoprotein, RpoE‑regulated |
| RA | 1,984,340 | G→A | 5.5% | L393L (TTG→TTA) | tyrP → | tyrosine transporter |
| RA | 2,011,734 | Δ1 bp | 100% | coding (308/444 nt) | fliJ → | flagellar protein |
| RA | 2,048,571 | A→T | 5.9% | P10P (CCA→CCT) | amn → | AMP nucleosidase |
| RA | 2,252,901 | A→C | 24.9% | intergenic (‑126/+297) | psuK ← / ← fruA | pseudouridine kinase/fused fructose‑specific PTS enzymes: IIBcomponent/IIC components |
| RA | 2,289,287 | C→A | 7.8% | P171P (CCG→CCT) | ccmC ← | heme exporter subunit |
| RA | 2,298,128 | C→T | 5.9% | intergenic (+256/+459) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,302,650 | C→A | 6.5% | M57I (ATG→ATT) | alkB ← | oxidative demethylase of N1‑methyladenine or N3‑methylcytosine DNA lesions |
| RA | 2,403,195 | G→T | 6.5% | S546* (TCG→TAG) | yfbS ← | putative transporter |
| RA | 2,407,141 | G→T | 13.8% | E65* (GAA→TAA) | ackA → | acetate kinase A and propionate kinase 2 |
| JC | 2,713,645 | +CCTGCGC | 61.9% | coding (334/2661 nt) | pka → | protein lysine acetyltransferase |
| RA | 2,719,426 | T→C | 100% | intergenic (‑321/+2) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,940,829 | A→T | 6.7% | intergenic (+7/‑27) | metZ → / → metW | tRNA‑Met/tRNA‑Met |
| RA | 2,982,873 | G→T | 6.4% | G71* (GGA→TGA) | yqeJ → | uncharacterized protein |
| RA | 3,020,228 | G→T | 9.6% | A368A (GCG→GCT) | guaD → | guanine deaminase |
| RA | 3,044,493 | A→C | 5.2% | L395W (TTG→TGG) | ubiI ← | 2‑octaprenylphenol hydroxylase, FAD‑dependent |
| RA | 3,080,865 | T→A | 25.9% | D267E (GAT→GAA) | metK → | S‑adenosylmethionine synthetase |
| RA | 3,103,319 | C→T | 10.3% | I136I (ATC→ATT) | yqgA → | DUF554 family putative inner membrane protein |
| RA | 3,246,908 | G→A | 9.2% | R222R (CGC→CGT) | yhaJ ← | LysR family putative transcriptional regulator |
| RA | 3,263,460 | C→A | 5.0% | intergenic (+499/+115) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,501,910 | G→A | 6.4% | H14Y (CAT→TAT) | php ← | phosphotriesterase homology protein |
| RA | 3,516,949 | C→A | 5.9% | F240L (TTC→TTA) | mrcA → | fused penicillin‑binding protein 1a: murein transglycosylase/murein transpeptidase |
| RA | 3,519,657 | G→T | 100% | intergenic (‑149/‑171) | nudE ← / → yrfF | adenosine nucleotide hydrolase; substrates include Ap3A, Ap2A, ADP‑ribose, NADH/inner membrane protein |
| RA | 3,526,702:1 | +C | 7.7% | coding (526/1623 nt) | pck → | phosphoenolpyruvate carboxykinase |
| RA | 3,553,566 | C→A | 17.0% | D134Y (GAT→TAT) | glpR ← | GlpR DNA‑binding transcriptional repressor |
| RA | 3,555,325 | T→C | 7.6% | intergenic (‑142/‑48) | glpE ← / → glpD | thiosulfate:cyanide sulfurtransferase (rhodanese)/sn‑glycerol‑3‑phosphate dehydrogenase, aerobic, FAD/NAD(P)‑binding |
| RA | 3,634,084 | C→T | 5.2% | intergenic (+179/‑138) | uspA → / → dtpB | universal stress global response regulator/dipeptide and tripeptide permease B |
| RA | 3,646,542 | C→A | 5.3% | S6I (AGC→ATC) | insH1 ← | IS5 transposase and trans‑activator |
| RA | 3,671,771 | T→A | 5.0% | intergenic (‑61/+9) | yhjG ← / ← yhjH | putative inner membrane‑anchored periplasmic AsmA family protein/cyclic‑di‑GMP phosphodiesterase, FlhDC‑regulated |
| RA | 3,721,480 | T→G | 7.8% | T418P (ACG→CCG) | xylB ← | xylulokinase |
| RA | 3,721,485 | T→G | 8.3% | Y416S (TAC→TCC) | xylB ← | xylulokinase |
| RA | 3,774,466 | G→C | 6.4% | intergenic (+89/‑109) | lldD → / → trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 3,774,518 | A→C | 17.5% | intergenic (+141/‑57) | lldD → / → trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 3,816,601 | A→T | 36.1% | H281L (CAC→CTC) | spoT → | bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
| RA | 3,868,359 | C→A | 6.9% | A54A (GCG→GCT) | dgoR ← | putative DNA‑binding transcriptional regulator |
| RA | 3,952,817 | T→G | 6.9% | intergenic (+12/+75) | ilvC → / ← ppiC | ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| RA | 3,960,036 | G→A | 9.8% | R87H (CGC→CAC) | rho → | transcription termination factor |
| RA | 4,064,048 | T→G | 5.5% | N357H (AAT→CAT) | yihS ← | aldose‑ketose isomerase; D‑mannose isomerase |
| RA | 4,071,350 | G→A | 23.7% | W181* (TGG→TAG) | yiiD → | putative acetyltransferase |
| RA | 4,297,846 | C→A | 9.0% | M150I (ATG→ATT) | alsE ← | allulose‑6‑phosphate 3‑epimerase |
| RA | 4,367,995 | G→A | 6.6% | P256L (CCC→CTC) | ampC ← | penicillin‑binding protein; beta‑lactamase, intrinsically weak |
| RA | 4,382,369 | T→A | 7.1% | intergenic (+5/‑31) | glyX → / → glyY | tRNA‑Gly/tRNA‑Gly |
| RA | 4,510,428 | G→T | 6.3% | intergenic (‑287/+60) | yjhU ← / ← yjhF | putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 373848 | 375112 | 1265 | 211 [205] | [210] 213 | frmA–[frmR] | frmA,[frmR] |
| * | * | ÷ | CP009273 | 4100624 | 4101504 | 881 | 213 [202] | [205] 211 | tpiA | tpiA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 360104 = | 286 (0.920) | 355 (1.140) | 169/278 | NT | 55.4% | intergenic (‑38/+557) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | = 360286 | NA (NA) | intergenic (‑220/+375) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor | |||||
| * | ? | CP009273 | = 360278 | NA (NA) | 9413 (32.020) +TTAATTAA |
197/262 | NT | 97.2% | intergenic (‑212/+383) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | = 361823 | 290 (0.930) | coding (831/834 nt) | mhpR | mhp operon transcriptional activator | |||||
| * | ? | CP009273 | 360652 = | 312 (1.000) | 8621 (41.440) +46 bp |
186/186 | NT | 97.9% | intergenic (‑586/+9) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | = 1317577 | 255 (0.820) | coding (101/882 nt) | yciV | PHP domain protein | |||||
| * | ? | CP009273 | 376716 = | NA (NA) | 23 (0.070) | 16/278 | NT | 6.8% | intergenic (‑1/‑91) | yaiX/insC1 | pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase/IS2 repressor TnpA |
| ? | CP009273 | 566411 = | 316 (1.010) | coding (63/552 nt) | ybcL | inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family | |||||
| * | ? | CP009273 | 376716 = | NA (NA) | 14 (0.040) | 11/278 | NT | 5.3% | intergenic (‑1/‑91) | yaiX/insC1 | pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase/IS2 repressor TnpA |
| ? | CP009273 | 1190448 = | 248 (0.790) | intergenic (‑41/‑131) | rluE/icd | 23S rRNA pseudouridine(2457) synthase/e14 prophage; isocitrate dehydrogenase, specific for NADP+ | |||||
| * | ? | CP009273 | = 378046 | NA (NA) | 27 (0.090) | 21/278 | NT | 7.9% | intergenic (+11/+1) | insD1/yaiX | IS2 transposase TnpB/pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase |
| ? | CP009273 | = 566415 | 315 (1.010) | coding (67/552 nt) | ybcL | inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family | |||||
| * | ? | CP009273 | 1203246 = | 74 (0.240) | 171 (0.620) | 103/246 | NT | 72.7% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 63 (0.230) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 75 (0.240) | 201 (0.730) | 109/246 | NT | 75.7% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 63 (0.230) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 2007609 | 213 (0.680) | 95 (0.320) | 58/266 | NT | 31.8% | coding (900/1659 nt) | fliF | flagellar basal‑body MS‑ring and collar protein |
| ? | CP009273 | 2021385 = | 203 (0.680) | coding (114/1695 nt) | yedQ | putative membrane‑anchored diguanylate cyclase | |||||
| * | ? | CP009273 | 3179455 = | NA (NA) | 39 (0.120) | 27/278 | NT | 9.0% | intergenic (+7/‑91) | yqiG/insC1 | pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein/IS2 repressor TnpA |
| ? | CP009273 | = 4118109 | 393 (1.260) | coding (215/318 nt) | metJ | transcriptional repressor, S‑adenosylmethionine‑binding | |||||
| * | ? | CP009273 | 4118105 = | 394 (1.260) | 34 (0.110) | 21/278 | NT | 7.9% | coding (219/318 nt) | metJ | transcriptional repressor, S‑adenosylmethionine‑binding |
| ? | CP009273 | = 4489328 | NA (NA) | intergenic (+11/+82) | insD1/yjgX | IS2 transposase TnpB/pseudogene fragment | |||||
| * | ? | CP009273 | 4532499 = | 285 (0.910) | 15 (0.050) | 11/260 | NT | 5.3% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | CP009273 | 4532813 = | 275 (0.940) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | CP009273 | = 4532507 | 293 (0.940) | 32 (0.110) | 20/260 | NT | 10.4% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | CP009273 | = 4532803 | 275 (0.940) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||