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 | annotation | gene | description |
| RA | 14,133 | C→T | intergenic (+54/‑35) | dnaK → / → dnaJ | chaperone protein DnaK/chaperone protein DnaJ |
| RA | 50,518 | A→G | G235G (GGT→GGC) | apaH ← | diadenosine tetraphosphatase |
| RA | 132,880 | T→C | R422R (CGT→CGC) | acnB → | hypothetical protein |
| RA | 136,437 | T→G | T10P (ACG→CCG) | speE ← | spermidine synthase |
| RA | 154,667 | T→C | T254A (ACG→GCG) | htrE ← | putative fimbrial usher protein HtrE |
| RA | 169,977 | A→G | E67G (GAG→GGG) | fhuC → | iron(III) hydroxamate ABC transporter ATP binding subunit |
| RA | 199,082 | T→C | G385G (GGT→GGC) | bamA → | outer membrane protein assembly factor BamA |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 288,948 | C→T | G72D (GGC→GAC) | xynR ← | CP4‑6 prophage; DNA‑binding transcriptional repressor XynR |
| RA | 324,226 | A→G | S157G (AGC→GGC) | ykgG → | DUF162 domain‑containing lactate utilization protein YkgG |
| RA | 338,266 | A→G | S497G (AGC→GGC) | yahF → | putative acyl‑CoA synthetase YahF |
| RA | 342,999 | T→C | V39A (GTT→GCT) | yahK → | aldehyde reductase, NADPH‑dependent |
| RA | 349,717 | T→C | intergenic (+145/‑295) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 360,285 | T→C | G98G (GGT→GGC) | cynX → | cyanate transporter |
| RA | 363,794 | T→C | T838A (ACG→GCG) | lacZ ← | beta‑galactosidase |
| RA | 388,700 | (G)5→4 | intergenic (+54/+53) | tauD → / ← hemB | taurine dioxygenase/porphobilinogen synthase |
| RA | 440,440 | A→G | V221A (GTT→GCT) | ispA ← | geranyl diphosphate/farnesyl diphosphate synthase |
| RA | 444,953 | A→G | T91A (ACC→GCC) | yajQ → | nucleotide binding protein |
| RA | 494,430 | A→G | Q9R (CAG→CGG) | recR → | DNA repair protein RecR |
| RA | 502,607 | A→G | V211A (GTG→GCG) | ybaL ← | putative transporter YbaL |
| RA | 513,158 | T→C | F195L (TTC→CTC) | ybaT → | putative transporter YbaT |
| RA | 519,790 | (G)5→4 | coding (58/687 nt) | ybbA → | putative ABC transporter ATP‑binding protein YbbA |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 529,867 | A→G | G50G (GGT→GGC) | ylbG ← | putative DNA‑binding transcriptional regulator YlbG |
| RA | 535,327 | T→C | V471A (GTC→GCC) | gcl → | glyoxylate carboligase |
| RA | 605,892 | T→C | intergenic (‑6/+59) | ybdF ← / ← ybdJ | PF04237 family protein YbdF/DUF1158 domain‑containing protein YbdJ |
| RA | 699,394 | C→G | intergenic (‑217/+180) | asnB ← / ← umpH | asparagine synthetase B/UMP phosphatase |
| RA | 704,018 | A→G | A25A (GCA→GCG) | nagE → | N‑acetylglucosamine specific PTS enzyme IIABC component |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 925,899 | (G)7→8 | noncoding (73/88 nt) | serW ← | tRNA‑Ser |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 936,504 | A→G | D1094G (GAC→GGC) | ftsK → | cell division DNA translocase FtsK |
| RA | 948,785 | T→C | T262A (ACA→GCA) | ycaN ← | putative LysR‑type transcriptional regulator YcaN |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,057,108 | A→G | E283G (GAA→GGA) | torT → | periplasmic trimethylamine‑N‑oxide binding protein |
| RA | 1,073,764 | T→C | N83S (AAC→AGC) | rutA ← | pyrimidine oxygenase |
| RA | 1,077,859 | A→G | Y342H (TAT→CAT) | putA ← | fused DNA‑binding transcriptional repressor/proline dehydrogenase/1‑pyrroline‑5‑carboxylate dehydrogenase PutA |
| RA | 1,111,354 | T→C | G164G (GGT→GGC) | opgH → | osmoregulated periplasmic glucans (OPGs) biosynthesis protein H |
| RA | 1,134,499 | T→C | V233A (GTG→GCG) | flgF → | flagellar basal‑body rod protein FlgF |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,187,710 | A→G | D177D (GAT→GAC) | roxA ← | ribosomal protein‑arginine oxygenase |
| RA | 1,212,088 | (C)8→9 | intergenic (‑85/+172) | iraM ← / ← ymgK | anti‑adaptor protein IraM, inhibitor of sigma(S) proteolysis/protein YmgK |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,227,593 | (G)6→7 | intergenic (‑121/‑88) | pliG ← / → ycgL | inhibitor of g‑type lysozyme/PF05166 family protein YcgL |
| RA | 1,227,625 | A→G | intergenic (‑153/‑56) | pliG ← / → ycgL | inhibitor of g‑type lysozyme/PF05166 family protein YcgL |
| RA | 1,254,499 | A→G | V485A (GTC→GCC) | ycgV ← | putative autotransporter adhesin YcgV |
| RA | 1,274,621 | C→T | P280S (CCT→TCT) | ychO → | putative invasin YchO |
| RA | 1,342,543 | A→G | E208G (GAA→GGA) | pyrF → | orotidine‑5'‑phosphate decarboxylase |
| RA | 1,351,067 | T→C | intergenic (‑28/+340) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase/DUF559 domain‑containing protein YcjD |
| RA | 1,351,196 | (G)7→9 | intergenic (‑157/+211) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase/DUF559 domain‑containing protein YcjD |
| RA | 1,399,013 | C→T | A172T (GCA→ACA) | fnr ← | DNA‑binding transcriptional dual regulator FNR |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,578,708 | A→G | V212A (GTG→GCG) | yddA ← | ABC transporter family protein YddA |
| RA | 1,594,132 | (C)8→7 | pseudogene (3955/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,622,393 | C→T | G354G (GGC→GGT) | ydeE → | dipeptide exporter |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,684,123 | T→C | G414G (GGT→GGC) | rstB → | sensory histidine kinase RstB |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,707,954 | T→C | L346L (TTG→CTG) | rsxC → | SoxR [2Fe‑2S] reducing system protein RsxC |
| RA | 1,811,557 | T→C | D208D (GAT→GAC) | tcyP → | cystine/sulfocysteine:cation symporter |
| RA | 1,833,991 | T→C | C197C (TGT→TGC) | ydjX → | DedA family protein YdjX |
| RA | 1,866,348 | T→C | Y42C (TAC→TGC) | mipA ← | scaffolding protein that interacts with murein polymerase and murein hydrolase |
| RA | 1,873,384 | A→G | K448K (AAA→AAG) | dgcJ → | putative diguanylate cyclase DgcJ |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,905,840 | G→A | P51P (CCG→CCA) | mntP → | Mn(2(+)) exporter |
| RA | 1,908,240 | T→C | intergenic (‑649/+21) | yobF ← / ← yebO | DUF2527 domain‑containing protein YobF/uncharacterized protein YebO |
| RA | 1,916,272 | A→G | T5T (ACA→ACG) | yebS → | intermembrane transport protein YebS |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,078,482 | A→G | intergenic (+348/‑93) | yeeW → / → yoeF | CP4‑44 prophage; putative uncharacterized protein YeeW/CP4‑44 prophage; putative uncharacterized protein YoeF |
| RA | 2,084,522 | A→G | L335P (CTT→CCT) | yeeE ← | inner membrane protein YeeE |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,186,163 | G→A | A83T (GCT→ACT) | rcnA → | Ni(2(+))/Co(2(+)) exporter |
| RA | 2,248,768 | T→C | D284G (GAC→GGC) | yeiE ← | putative LysR‑type transcriptional regulator YeiE |
| RA | 2,250,058 | T→C | S114S (AGT→AGC) | yeiH → | conserved inner membrane protein YeiH |
| RA | 2,291,549 | T→C | T288A (ACG→GCG) | ccmH ← | holocytochrome c synthetase ‑ thiol:disulfide oxidoreductase CcmH |
| RA | 2,326,867 | T→C | G253G (GGT→GGC) | atoB → | acetyl‑CoA acetyltransferase |
| RA | 2,399,580 | T→C | N196D (AAC→GAC) | nuoG ← | NADH:quinone oxidoreductase subunit G |
| RA | 2,403,725 | T→C | T41A (ACC→GCC) | nuoC ← | NADH:quinone oxidoreductase subunit CD |
| RA | 2,413,442 | (T)7→6 | intergenic (‑310/‑28) | yfbV ← / → ackA | UPF0208 membrane protein YfbV/acetate kinase |
| RA | 2,414,193 | A→G | T242A (ACC→GCC) | ackA → | acetate kinase |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,456,257 | A→G | intergenic (‑611/+70) | yfcV ← / ← sixA | putative fimbrial protein YfcV/phosphohistidine phosphatase |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,556,929 | T→C | V123V (GTA→GTG) | eutC ← | ethanolamine ammonia‑lyase subunit beta |
| RA | 2,571,276 | +G | coding (476/1404 nt) | eutE ← | putative aldehyde dehydrogenase, ethanolamine utilization protein |
| RA | 2,595,690 | T→C | E57G (GAA→GGA) | tmcA ← | tRNA(Met) cytidine acetyltransferase |
| RA | 2,653,266 | A→G | N258S (AAC→AGC) | sseA → | 3‑mercaptopyruvate sulfurtransferase |
| RA | 2,656,109 | T→C | T84A (ACG→GCG) | pepB ← | aminopeptidase B |
| RA | 2,706,111 | G→A | F338F (TTC→TTT) | lepA ← | elongation factor 4 |
| RA | 2,723,402 | G→A | A226T (GCT→ACT) | pssA → | phosphatidylserine synthase |
| RA | 2,723,976 | A→G | H417R (CAC→CGC) | pssA → | phosphatidylserine synthase |
| RA | 2,766,322 | T→C | H135H (CAT→CAC) | rnlA → | CP4‑57 prophage; RNase LS, toxin of the RnlAB toxin‑antitoxin system |
| RA | 2,775,097 | G→A | intergenic (+76/‑448) | yfjW → / → ypjI | CP4‑57 prophage; uncharacterized protein YfjW/putative UPF0401 protein YpjI |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,819,719 | C→T | A765T (GCA→ACA) | alaS ← | alanine‑‑tRNA ligase/DNA‑binding transcriptional repressor |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,870,786 | (C)5→4 | coding (519/1050 nt) | truD ← | tRNA pseudouridine(13) synthase |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,141,415 | T→A | T525T (ACA→ACT) | hybC ← | hydrogenase 2 large subunit |
| RA | 3,195,947 | G→A | V269V (GTC→GTT) | rfaE ← | fused heptose 7‑phosphate kinase/heptose 1‑phosphate adenyltransferase |
| RA | 3,234,267 | C→T | G63G (GGG→GGA) | higB ← | ribosome‑dependent mRNA interferase toxin HigB |
| RA | 3,240,984 | (G)7→8 | coding (1041/1245 nt) | sstT → | serine/threonine:Na(+) symporter |
| RA | 3,255,657 | G→A | A332V (GCC→GTC) | cyuA ← | putative L‑cysteine desulfidase CyuA |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,390,531 | A→G | intergenic (+82/+52) | aaeR → / ← tldD | LysR‑type transcriptional regulator AaeR/metalloprotease TldD |
| RA | 3,449,313 | T→C | T191A (ACC→GCC) | rpsC ← | 30S ribosomal subunit protein S3 |
| RA | 3,548,181 | A→G | S630S (AGT→AGC) | malQ ← | 4‑alpha‑glucanotransferase |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,592,219 | T→C | E36G (GAA→GGA) | ugpB ← | sn‑glycerol 3‑phosphate ABC transporter periplasmic binding protein |
| RA | 3,677,573 | T→C | T260A (ACC→GCC) | yhjG ← | AsmA family protein YhjG |
| RA | 3,699,922 | (C)6→7 | intergenic (+29/+58) | bcsG → / ← ldrD | cellulose phosphoethanolamine transferase/small toxic polypeptide LdrD |
| RA | 3,719,070 | (A)7→6 | intergenic (‑26/‑408) | yiaF ← / → yiaG | DUF3053 domain‑containing protein YiaF/putative DNA‑binding transcriptional regulator YiaG |
| RA | 3,759,146 | A→G | L239P (CTT→CCT) | selB ← | selenocysteyl‑tRNA‑specific translation elongation factor |
| RA | 3,765,681 | T→C | C1167R (TGC→CGC) | rhsA → | rhs element protein RhsA |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,882,136 | T→C | P62P (CCA→CCG) | dnaN ← | beta sliding clamp |
| RA | 3,886,501 | T→C | F476L (TTC→CTC) | yidC → | membrane protein insertase YidC |
| RA | 3,903,744 | T→C | E618E (GAA→GAG) | bglF ← | beta‑glucoside specific PTS enzyme II/BglG kinase/BglG phosphatase |
| RA | 3,930,087 | A→G | L336S (TTA→TCA) | ravA ← | regulatory ATPase RavA |
| RA | 3,957,568 | G→A | Q85* (CAA→TAA) | ilvY ← | DNA‑binding transcriptional dual regulator IlvY |
| RA | 3,995,913 | C→T | R111C (CGC→TGC) | yigA → | conserved protein YigA |
| RA | 4,077,790 | T→C | R114R (CGT→CGC) | yiiD → | putative acetyltransferase YiiD |
| RA | 4,101,728 | (G)7→8 | coding (39/984 nt) | kdgT → | 2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| RA | 4,108,469 | T→C | R306R (CGT→CGC) | pfkA → | 6‑phosphofructokinase I |
| RA | 4,108,850 | T→C | V6A (GTA→GCA) | sbp → | sulfate/thiosulfate ABC transporter periplasmic binding protein Sbp |
| RA | 4,163,366 | A→G | intergenic (‑96/‑273) | trmA ← / → btuB | tRNA m(5)U54 methyltransferase/cobalamin/cobinamide outer membrane transporter |
| RA | 4,189,398 | A→G | N1350S (AAC→AGC) | rpoC → | RNA polymerase subunit beta' |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,318,564 | A→G | R67R (CGT→CGC) | phnK ← | carbon‑phosphorus lyase subunit PhnK |
| RA | 4,326,695 | T→C | T14A (ACC→GCC) | yjdM ← | conserved protein YjdM |
| RA | 4,361,448 | (A)8→7 | coding (487/1539 nt) | cadC ← | DNA‑binding transcriptional activator CadC |
| RA | 4,408,721 | C→T | R690C (CGC→TGC) | rnr → | RNase R |
| RA | 4,414,597 | A→G | D108G (GAC→GGC) | aidB → | putative acyl‑CoA dehydrogenase AidB |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,510,129 | T→C | pseudogene (326/330 nt) | yjhV → | KpLE2 phage‑like element; putative uncharacterized protein YjhV |
| RA | 4,571,858 | G→A | Q36Q (CAG→CAA) | yjiS → | DUF1127 domain‑containing protein YjiS |
| RA | 4,597,472 | T→C | N657S (AAC→AGC) | opgB ← | phosphoglycerol transferase I |
| RA | 4,601,309 | T→C | D70G (GAC→GGC) | dnaT ← | primosomal protein DnaT |
| RA | 4,606,094 | (G)8→7 | noncoding (72/87 nt) | leuV ← | tRNA‑Leu |
| RA | 4,606,330 | (G)8→9 | noncoding (72/87 nt) | leuQ ← | tRNA‑Leu |
| RA | 4,609,336 | (C)7→9 | intergenic (+13/‑78) | yjjG → / → prfC | pyrimidine nucleotidase/peptide chain release factor RF3 |
| RA | 4,625,760 | A→G | Y289C (TAC→TGC) | serB → | phosphoserine phosphatase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 271495–271582 | 271644–271587 | 6–150 | 19 [18] | [18] 19 | insI‑1 | IS30 transposase |
| * | * | ÷ | NC_000913 | 737540–737669 | 737733 | 65–194 | 19 [18] | [18] 19 | ybfL | putative transposase YbfL |
| * | * | ÷ | NC_000913 | 3423783–3424234 | 3424523–3424238 | 5–741 | 19 [18] | [10] 19 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 59 (0.700) | 43 (0.580) | 30/244 | 1.0 | 43.6% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 59 (0.800) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 59 (0.700) | 21 (0.280) | 17/244 | 2.4 | 27.4% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 59 (0.800) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 90 (1.100) | 60/268 | 0.1 | 100% | intergenic (+253/‑33) | ychE/insH21 | putative inner membrane protein/IS5 transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 3363001 = | 148 (1.760) | 117 (1.400) | 56/274 | 0.2 | 61.3% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 1 (0.010) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 109 (1.300) | 65/276 | 0.1 | 97.3% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 3 (0.040) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 4542690 | 47 (0.560) | 34 (0.430) | 27/258 | 1.4 | 40.3% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 57 (0.730) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||