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 | 87,881 | A→G | 5.3% | intergenic (+33/‑147) | ilvH → / → cra | acetolactate synthase 3, small subunit, valine‑sensitive/transcriptional repressor‑activator for carbon metabolism |
| RA | 87,884 | T→A | 6.3% | intergenic (+36/‑144) | ilvH → / → cra | acetolactate synthase 3, small subunit, valine‑sensitive/transcriptional repressor‑activator for carbon metabolism |
| RA | 164,581 | A→C | 19.0% | intergenic (+47/‑149) | hrpB → / → mrcB | putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase |
| RA | 222,958 | Δ1 bp | 100% | coding (126/576 nt) | gmhB → | D,D‑heptose 1,7‑bisphosphate phosphatase |
| RA | 255,349 | G→A | 5.2% | A123V (GCG→GTG) | pepD ← | aminoacyl‑histidine dipeptidase (peptidase D) |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 292,302 | C→G | 5.7% | intergenic (+71/+20) | yagJ → / ← yagK | CP4‑6 prophage; uncharacterized protein;Phage or Prophage Related/CP4‑6 prophage; conserved protein |
| RA | 329,503 | A→G | 5.4% | N14S (AAT→AGT) | betT → | choline transporter of high affinity |
| RA | 329,509 | T→C | 5.1% | V16A (GTG→GCG) | betT → | choline transporter of high affinity |
| RA | 329,512 | T→A | 5.2% | V17E (GTG→GAG) | betT → | choline transporter of high affinity |
| RA | 329,514 | T→G | 5.2% | F18V (TTT→GTT) | betT → | choline transporter of high affinity |
| RA | 329,519 | C→A | 5.1% | Y19* (TAC→TAA) | betT → | choline transporter of high affinity |
| RA | 329,521 | C→A | 5.1% | T20N (ACC→AAC) | betT → | choline transporter of high affinity |
| RA | 508,986 | C→T | 6.1% | P798P (CCG→CCA) | copA ← | copper transporter |
| RA | 543,091 | G→C | 10.3% | intergenic (+58/+170) | glxK → / ← allE | glycerate kinase II/S‑ureidoglycine aminohydrolase |
| RA | 543,094 | G→C | 9.4% | intergenic (+61/+167) | glxK → / ← allE | glycerate kinase II/S‑ureidoglycine aminohydrolase |
| RA | 551,432 | C→A | 5.2% | intergenic (+100/+95) | ybcF → / ← purK | putative carbonate kinase/N5‑carboxyaminoimidazole ribonucleotide synthase |
| RA | 593,472 | G→T | 5.7% | R433R (CGC→CGA) | cusS ← | copper‑sensing histidine kinase in two‑component regulatory system with CusR |
| RA | 658,952 | T→C | 6.5% | G2G (GGT→GGC) | tatE → | TatABCE protein translocation system subunit |
| RA | 681,694 | A→G | 6.5% | intergenic (+31/+29) | djlC → / ← hscC | J domain‑containing HscC co‑chaperone; Hsc56/Hsp70 family chaperone Hsc62; RpoD‑binding transcription inhibitor |
| RA | 681,699 | T→A | 6.1% | intergenic (+36/+24) | djlC → / ← hscC | J domain‑containing HscC co‑chaperone; Hsc56/Hsp70 family chaperone Hsc62; RpoD‑binding transcription inhibitor |
| RA | 681,700 | T→A | 6.1% | intergenic (+37/+23) | djlC → / ← hscC | J domain‑containing HscC co‑chaperone; Hsc56/Hsp70 family chaperone Hsc62; RpoD‑binding transcription inhibitor |
| RA | 681,705 | C→T | 6.2% | intergenic (+42/+18) | djlC → / ← hscC | J domain‑containing HscC co‑chaperone; Hsc56/Hsp70 family chaperone Hsc62; RpoD‑binding transcription inhibitor |
| RA | 781,238 | T→A | 7.9% | intergenic (+16/‑131) | lysY → / → lysZ | tRNA‑Lys/tRNA‑Lys |
| RA | 826,945 | A→G | 5.9% | L103P (CTG→CCG) | ybhS ← | putative ABC transporter permease |
| RA | 1,151,873 | T→A | 5.4% | intergenic (+22/‑66) | acpP → / → fabF | acyl carrier protein (ACP)/3‑oxoacyl‑[acyl‑carrier‑protein] synthase II |
| RA | 1,151,874 | T→A | 6.0% | intergenic (+23/‑65) | acpP → / → fabF | acyl carrier protein (ACP)/3‑oxoacyl‑[acyl‑carrier‑protein] synthase II |
| RA | 1,287,149 | G→A | 8.0% | noncoding (88/171 nt) R10* (CGA→TGA) |
rttR ← tpr ← |
rtT sRNA, processed from tyrT transcript protamine‑like protein |
| RA | 1,289,573 | C→T | 5.3% | A110V (GCG→GTG) | rssA → | putative patatin‑like family phospholipase |
| RA | 1,351,222 | T→A | 14.1% | intergenic (‑183/+185) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/DUF559 family endonuclease‑related protein |
| RA | 1,351,228 | G→C | 10.1% | intergenic (‑189/+179) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/DUF559 family endonuclease‑related protein |
| RA | 1,371,830 | A→T | 5.2% | S539C (AGT→TGT) | ycjM → | alpha amylase catalytic domain family protein |
| RA | 1,376,954 | T→A | 5.4% | C41* (TGT→TGA) | ycjS → | putative NADH‑binding oxidoreductase |
| RA | 1,379,017 | A→C | 5.4% | L378L (CTA→CTC) | ycjT → | putative family 65 glycosyl hydrolase |
| RA | 1,466,336 | C→G | 5.2% | pseudogene (945/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,504 | A→G | 7.0% | pseudogene (1113/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,856 | A→G | 5.1% | pseudogene (1465/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,743,931 | C→T | 12.0% | P159S (CCG→TCG) | mdtK → | multidrug efflux system transporter |
| RA | 1,758,946 | G→T | 8.2% | L115L (CTC→CTA) | sufE ← | sulfur acceptor protein |
| RA | 1,788,194 | G→A | 5.5% | P250P (CCG→CCA) | ppsR → | PEP synthase kinase and PEP synthase pyrophosphorylase |
| RA | 1,864,768 | T→C | 8.8% | intergenic (+34/+14) | yeaD → / ← yeaE | D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent |
| RA | 1,883,027 | C→G | 5.2% | intergenic (+30/‑161) | dmlA → / → yeaV | D‑malate oxidase, NAD‑dependent; putative tartrate dehydrogenase/putative transporter |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 1,980,110 | T→G | 5.9% | S120A (TCC→GCC) | uspC → | universal stress protein |
| RA | 2,019,460 | G→A | 100% | V359I (GTC→ATC) | fliK → | flagellar hook‑length control protein |
| RA | 2,089,203 | G→T | 5.9% | intergenic (‑75/+8) | yeeZ ← / ← yoeB | putative epimerase/toxin of the YoeB‑YefM toxin‑antitoxin system |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,177,279 | C→A | 8.7% | intergenic (‑75/+233) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,206,622 | A→G | 6.4% | T310A (ACA→GCA) | yehM → | uncharacterized protein |
| RA | 2,229,177 | A→C | 23.7% | intergenic (+112/+261) | yohP → / ← dusC | uncharacterized protein/tRNA‑dihydrouridine synthase C |
| RA | 2,282,830 | T→C | 6.9% | intergenic (+29/+110) | rplY → / ← yejK | 50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein |
| RA | 2,282,831 | C→G | 6.9% | intergenic (+30/+109) | rplY → / ← yejK | 50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein |
| RA | 2,282,832 | C→G | 7.4% | intergenic (+31/+108) | rplY → / ← yejK | 50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein |
| RA | 2,282,833 | G→A | 7.4% | intergenic (+32/+107) | rplY → / ← yejK | 50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein |
| RA | 2,304,459 | C→T | 6.4% | intergenic (+66/+649) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,649 | C→T | 18.5% | intergenic (+256/+459) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,988 | T→C | 6.4% | intergenic (+595/+120) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| JC JC | 2,375,828 | IS186 (+) +4 bp | 100% | coding (132‑135/963 nt) | menC ← | O‑succinylbenzoyl‑CoA synthase |
| RA | 2,653,692 | A→T | 5.9% | intergenic (+353/‑163) | sseA → / → ryfA | 3‑mercaptopyruvate sulfurtransferase/novel sRNA, function unknown |
| RA | 2,653,693 | A→G | 6.0% | intergenic (+354/‑162) | sseA → / → ryfA | 3‑mercaptopyruvate sulfurtransferase/novel sRNA, function unknown |
| RA | 2,653,695 | A→T | 6.0% | intergenic (+356/‑160) | sseA → / → ryfA | 3‑mercaptopyruvate sulfurtransferase/novel sRNA, function unknown |
| RA | 2,653,697 | C→T | 5.7% | intergenic (+358/‑158) | sseA → / → ryfA | 3‑mercaptopyruvate sulfurtransferase/novel sRNA, function unknown |
| RA | 2,653,698 | A→T | 6.2% | intergenic (+359/‑157) | sseA → / → ryfA | 3‑mercaptopyruvate sulfurtransferase/novel sRNA, function unknown |
| RA | 2,663,466 | G→T | 5.3% | V9L (GTG→TTG) | suhB → | inositol monophosphatase |
| RA | 2,663,482 | A→C | 5.2% | K14T (AAG→ACG) | suhB → | inositol monophosphatase |
| RA | 2,716,030 | T→G | 6.1% | intergenic (+20/+36) | eamB → / ← grcA | cysteine and O‑acetylserine exporter/autonomous glycyl radical cofactor |
| RA | 2,716,033 | C→A | 6.2% | intergenic (+23/+33) | eamB → / ← grcA | cysteine and O‑acetylserine exporter/autonomous glycyl radical cofactor |
| RA | 2,726,043 | G→T | 7.9% | intergenic (‑297/+26) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,726,044 | T→G | 7.0% | intergenic (‑298/+25) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,726,045 | C→A | 7.3% | intergenic (‑299/+24) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,726,046 | A→C | 7.4% | intergenic (‑300/+23) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,739,179 | A→G | 5.7% | A297A (GCT→GCC) | tyrA ← | fused chorismate mutase T/prephenate dehydrogenase |
| RA | 2,768,614 | A→C | 5.2% | intergenic (+41/‑51) | yfjP → / → yfjQ | CP4‑57 prophage; 50S ribosome‑binding GTPase family protein/CP4‑57 prophage; uncharacterized protein |
| RA | 2,778,825 | A→G | 5.0% | I1301T (ATT→ACT) | ypjA ← | adhesin‑like autotransporter |
| RA | 2,818,046 | A→G | 6.7% | intergenic (‑186/+13) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,818,049 | T→A | 6.5% | intergenic (‑189/+10) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,904,212 | G→A | 100% | intergenic (+838/+535) | ygcE → / ← queE | putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis |
| RA | 2,977,039 | C→G | 5.3% | I147M (ATC→ATG) | galR → | galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor |
| RA | 3,121,445 | T→C | 8.7% | intergenic (‑166/+189) | glcA ← / ← glcB | glycolate transporter/malate synthase G |
| RA | 3,156,591 | T→G | 6.0% | intergenic (+73/‑32) | yqhD → / → dkgA | aldehyde reductase, NADPH‑dependent/2,5‑diketo‑D‑gluconate reductase A |
| RA | 3,270,182 | C→T | 6.8% | intergenic (+580/+34) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,291,109 | A→T | 5.1% | K766* (AAA→TAA) ‡ | yraJ → | putative outer membrane protein |
| RA | 3,291,110 | A→T | 5.3% | K766I (AAA→ATA) ‡ | yraJ → | putative outer membrane protein |
| RA | 3,299,627 | C→T | 6.6% | A97T (GCG→ACG) | yhbP ← | UPF0306 family protein |
| RA | 3,539,805 | G→A | 5.6% | intergenic (+99/‑358) | yhgF → / → feoA | putative transcriptional accessory protein/ferrous iron transporter, protein A |
| RA | 3,539,815 | A→T | 5.5% | intergenic (+109/‑348) | yhgF → / → feoA | putative transcriptional accessory protein/ferrous iron transporter, protein A |
| RA | 3,539,816 | T→A | 5.7% | intergenic (+110/‑347) | yhgF → / → feoA | putative transcriptional accessory protein/ferrous iron transporter, protein A |
| RA | 3,539,817 | A→T | 5.4% | intergenic (+111/‑346) | yhgF → / → feoA | putative transcriptional accessory protein/ferrous iron transporter, protein A |
| RA | 3,539,827 | T→C | 6.1% | intergenic (+121/‑336) | yhgF → / → feoA | putative transcriptional accessory protein/ferrous iron transporter, protein A |
| RA | 3,560,455:1 | +G | 100% | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,828,980 | A→C | 6.7% | Q12H (CAA→CAC) | xanP → | xanthine permease |
| JC JC | 3,890,075 | IS5 (–) +4 bp | 100% | coding (1346‑1349/1416 nt) | tnaA → | tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent |
| RA | 3,908,507 | T→G | 6.6% | intergenic (‑141/+42) | pstB ← / ← pstA | phosphate ABC transporter ATPase/phosphate ABC transporter permease |
| RA | 4,153,616 | C→T | 5.1% | intergenic (‑518/+80) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,274,740 | G→A | 6.7% | intergenic (+79/+20) | ssb → / ← yjcB | single‑stranded DNA‑binding protein/putative inner membrane protein |
| RA | 4,274,742 | T→A | 6.6% | intergenic (+81/+18) | ssb → / ← yjcB | single‑stranded DNA‑binding protein/putative inner membrane protein |
| RA | 4,274,744 | T→C | 6.6% | intergenic (+83/+16) | ssb → / ← yjcB | single‑stranded DNA‑binding protein/putative inner membrane protein |
| RA | 4,296,060 | C→T | 32.0% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,362,581 | C→A | 86.3% | noncoding (46/76 nt) | pheU ← | tRNA‑Phe |
| RA | 4,379,044 | A→G | 5.4% | L108P (CTG→CCG) | frdD ← | fumarate reductase (anaerobic), membrane anchor subunit |
| RA | 4,406,129 | T→C | 100% | intergenic (+144/‑61) | purA → / → nsrR | adenylosuccinate synthetase/nitric oxide‑sensitive repressor for NO regulon |
| RA | 4,448,423 | T→A | 5.2% | intergenic (+188/‑24) | ytfP → / → chpS | GGCT‑like protein/antitoxin of the ChpBS toxin‑antitoxin system |
| RA | 4,448,424 | T→A | 5.2% | intergenic (+189/‑23) | ytfP → / → chpS | GGCT‑like protein/antitoxin of the ChpBS toxin‑antitoxin system |
| RA | 4,448,425 | T→A | 5.2% | intergenic (+190/‑22) | ytfP → / → chpS | GGCT‑like protein/antitoxin of the ChpBS toxin‑antitoxin system |
| JC JC | 4,640,551 | IS1 (–) +9 bp | 100% | intergenic (+9/‑383) | yjjY → / → yjtD | uncharacterized protein/putative methyltransferase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 773004 | 774208 | 1205 | 59 [55] | [53] 59 | [cydA]–[cydX] | [cydA],cydB,[cydX] |
| * | * | ÷ | NC_000913 | 1037684 | 1039324 | 1641 | 59 [57] | [55] 58 | cbdA–[cbdB] | cbdA,[cbdB] |
| * | * | ÷ | NC_000913 | 1166031 | 1167421 | 1391 | 60 [57] | [55] 58 | ndh | ndh |
| * | * | ÷ | NC_000913 | 3423716–3424542 | 3424542 | 1–827 | 59 [57] | [57] 62 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 39200 | NA (NA) | 3 (0.020) | 3/264 | NT | NA | noncoding (50/82 nt) | REP4 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP4 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913 | = 39232 | NA (NA) | noncoding (82/82 nt) | REP4 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP4 (repetitive extragenic palindromic) element; contains 2 REP sequences | |||||
| * | ? | NC_000913 | 263234 = | 158 (1.120) | 20 (0.140) | 5/272 | NT | 11.5% | intergenic (‑22/+94) | ykfN/ykfI | pseudogene, YdiA family/CP4‑6 prophage; toxin of the YkfI‑YafW toxin‑antitoxin system |
| ? | NC_000913 | 263267 = | 154 (1.110) | intergenic (‑55/+61) | ykfN/ykfI | pseudogene, YdiA family/CP4‑6 prophage; toxin of the YkfI‑YafW toxin‑antitoxin system | |||||
| * | ? | NC_000913 | 781369 = | 112 (0.790) | 19 (0.140) +GAG |
12/272 | NT | 14.7% | noncoding (1/76 nt) | lysZ | tRNA‑Lys |
| ? | NC_000913 | = 2521006 | 114 (0.810) | noncoding (76/76 nt) | valU | tRNA‑Val | |||||
| * | ? | NC_000913 | = 1097101 | 69 (0.490) | 8 (0.060) | 3/262 | NT | 10.5% | intergenic (+272/+464) | ycdU/serX | putative inner membrane protein/tRNA‑Ser |
| ? | NC_000913 | = 1097105 | 72 (0.540) | intergenic (+276/+460) | ycdU/serX | putative inner membrane protein/tRNA‑Ser | |||||
| * | ? | NC_000913 | 1207790 = | 48 (0.340) | 55 (0.440) | 34/246 | NT | 53.0% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 55 (0.440) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 49 (0.350) | 65 (0.520) | 36/246 | NT | 56.9% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 55 (0.440) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 110 (0.800) | 53/270 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 2354657 | 192 (1.360) | 11 (0.080) | 4/274 | NT | 5.5% | coding (393/1260 nt) | glpB | anaerobic sn‑glycerol‑3‑phosphate dehydrogenase membrane anchor subunit |
| ? | NC_000913 | = 2354704 | 189 (1.350) | coding (440/1260 nt) | glpB | anaerobic sn‑glycerol‑3‑phosphate dehydrogenase membrane anchor subunit | |||||