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 | 10,320 | (T)6→7 | coding (175/567 nt) | satP ← | acetate/succinate:H(+) symporter |
| RA | 28,965 | A→G | T198A (ACC→GCC) | dapB → | 4‑hydroxy‑tetrahydrodipicolinate reductase |
| RA | 82,813 | A→G | C239C (TGT→TGC) | leuA ← | 2‑isopropylmalate synthase |
| RA | 198,447 | T→C | S174P (TCA→CCA) | bamA → | outer membrane protein assembly factor BamA |
| RA | 222,866 | C→T | R12C (CGT→TGT) | gmhB → | D‑glycero‑beta‑D‑manno‑heptose‑1,7‑bisphosphate 7‑phosphatase |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 265,792 | G→A | S99F (TCC→TTC) | ykfB ← | CP4‑6 prophage; protein YkfB |
| RA | 305,502 | C→T | R439H (CGC→CAC) | ecpD ← | fimbrial adhesin EcpD |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 561,193 | A→G | E499E (GAA→GAG) | sfmD → | putative fimbrial usher protein SfmD |
| RA | 568,610 | T→C | L99S (TTG→TCG) | emrE → | multidrug/betaine/choline efflux transporter EmrE |
| RA | 609,652 | G→A | A143V (GCG→GTG) | entD ← | phosphopantetheinyl transferase EntD |
| RA | 713,956 | A→G | K133K (AAA→AAG) | pgm → | phosphoglucomutase |
| RA | 730,917 | T→C | S445S (AGT→AGC) | rhsC → | rhs element protein RhsC |
| RA | 731,057 | G→T | W492L (TGG→TTG) | rhsC → | rhs element protein RhsC |
| RA | 731,392 | A→G | T604A (ACC→GCC) | rhsC → | rhs element protein RhsC |
| RA | 731,472 | T→G | G630G (GGT→GGG) | rhsC → | rhs element protein RhsC |
| RA | 731,475 | G→A | L631L (CTG→CTA) | rhsC → | rhs element protein RhsC |
| RA | 733,230 | A→G | R1216R (CGA→CGG) | rhsC → | rhs element protein RhsC |
| RA | 733,260 | A→G | K1226K (AAA→AAG) | rhsC → | rhs element protein RhsC |
| RA | 814,784 | A→G | D420G (GAC→GGC) | uvrB → | excision nuclease subunit B |
| RA | 824,247 | C→T | G84D (GGT→GAT) | ybhP ← | endonuclease/exonuclease/phosphatase domain‑containing protein YbhP |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 913,007 | T→C | T270A (ACC→GCC) | hcp ← | protein S‑nitrosylase |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 987,789 | A→G | R399R (CGT→CGC) | asnS ← | asparagine‑‑tRNA ligase |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,015,515 | (T)7→8 | intergenic (+56/‑200) | pqiC → / → rmf | intermembrane transport lipoprotein PqiC/ribosome modulation factor |
| RA | 1,070,462 | T→C | K165R (AAG→AGG) | rutE ← | putative malonic semialdehyde reductase |
| RA | 1,097,218 | (G)7→8 | intergenic (+389/+347) | ycdU → / ← serX | uncharacterized protein YcdU/tRNA‑Ser |
| RA | 1,108,087 | C→T | W285* (TGG→TGA) | opgC ← | protein required for succinyl modification of osmoregulated periplasmic glucans |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,257,285 | A→G | G176G (GGT→GGC) | ychF ← | redox‑responsive ATPase YchF |
| RA | 1,302,144 | A→G | L321L (CTA→CTG) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,428,487 | G→A | A80A (GCC→GCT) | insH‑5 ← | Rac prophage; IS5 transposase and trans‑activator |
| RA | 1,428,499 | G→C | A76A (GCC→GCG) | insH‑5 ← | Rac prophage; IS5 transposase and trans‑activator |
| RA | 1,428,502 | A→G | G75G (GGT→GGC) | insH‑5 ← | Rac prophage; IS5 transposase and trans‑activator |
| RA | 1,428,505 | G→A | D74D (GAC→GAT) | insH‑5 ← | Rac prophage; IS5 transposase and trans‑activator |
| RA | 1,431,830 | G→A | A928T (GCT→ACT) | stfR → | Rac prophage; putative membrane protein |
| RA | 1,519,731 | A→G | L235L (CTA→CTG) | curA → | NADPH‑dependent curcumin/dihydrocurcumin reductase |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,594,256 | (C)8→9 | pseudogene (3831/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,708,901 | A→T | R661R (CGA→CGT) | rsxC → | SoxR [2Fe‑2S] reducing system protein RsxC |
| RA | 1,708,985 | G→C | A689A (GCG→GCC) | rsxC → | SoxR [2Fe‑2S] reducing system protein RsxC |
| RA | 1,763,098 | A→G | R304R (CGT→CGC) | sufB ← | Fe‑S cluster scaffold complex subunit SufB |
| RA | 1,769,478 | (G)7→8 | coding (405/1113 nt) | ydiK → | putative transporter YdiK |
| 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 | 1,952,700 | T→C | intergenic (+39/‑2) | yecN → / → cmoA | putative inner membrane protein/carboxy‑S‑adenosyl‑L‑methionine synthase |
| RA | 1,971,142 | G→A | A517V (GCC→GTC) | tar ← | methyl‑accepting chemotaxis protein Tar |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,021,446 | T→C | V120A (GTG→GCG) | fliN → | flagellar motor switch protein FliN |
| RA | 2,044,622 | C→T | noncoding (74/76 nt) | asnT → | tRNA‑Asn |
| RA | 2,079,953 | C→G | M213I (ATG→ATC) | yeeA ← | putative transporter YeeA |
| RA | 2,158,571 | C→T | S62S (TCC→TCT) | mdtC → | multidrug efflux pump RND permease subunit MdtC |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,200,203 | G→A | intergenic (+2905/‑76) | yehF → / → yehI | putative protein YehF/DUF4132 domain‑containing protein YehI |
| RA | 2,236,511 | G→A | intergenic (+11/+232) | preA → / ← mglC | NAD‑dependent dihydropyrimidine dehydrogenase subunit PreA/D‑galactose/methyl‑galactoside ABC transporter membrane subunit |
| JC JC | 2,375,828 | IS186 (–) +4 bp | coding (132‑135/963 nt) | menC ← | o‑succinylbenzoate synthase |
| RA | 2,421,876 | C→T | L57F (CTC→TTC) | yfcH → | putative NAD‑dependent epimerase YfcH |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,455,599 | G→A | G16G (GGC→GGT) | yfcV ← | putative fimbrial protein YfcV |
| RA | 2,462,889 | (C)9→8 | intergenic (+243/‑123) | fadL → / → yfdF | long‑chain fatty acid outer membrane channel/bacteriophage T2 receptor/protein YfdF |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,740,435 | G→A | A239V (GCG→GTG) | aroF ← | 3‑deoxy‑7‑phosphoheptulonate synthase, Tyr‑sensitive |
| RA | 2,759,677 | C→T | V231V (GTC→GTT) | yfjI → | CP4‑57 prophage; protein YfjI |
| RA | 2,765,794 | (C)7→8 | intergenic (‑18/‑124) | yfjM ← / → rnlA | CP4‑57 prophage; protein YfjM/CP4‑57 prophage; RNase LS, toxin of the RnlAB toxin‑antitoxin system |
| RA | 2,783,288 | G→A | pseudogene (17/240 nt) | pinH ← | putative invertase fragment |
| RA | 2,805,026 | T→C | V71A (GTA→GCA) | proV → | glycine betaine ABC transporter ATP binding subunit ProV |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,947,343 | (A)8→7 | intergenic (‑165/‑44) | mltA ← / → metZ | membrane‑bound lytic murein transglycosylase A/tRNA‑Met |
| 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 | 3,086,309 | G→A | R41R (CGG→CGA) | yqgC → | protein YqgC |
| RA | 3,353,093 | T→C | intergenic (‑68/+28) | arcB ← / ← yhcC | sensory histidine kinase ArcB/radical SAM family oxidoreductase YhcC |
| 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 | 3,449,796 | C→T | A30T (GCT→ACT) | rpsC ← | 30S ribosomal subunit protein S3 |
| RA | 3,457,884 | T→C | V503A (GTG→GCG) | gspD → | Type II secretion system protein GspD |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,626,974 | T→C | G855G (GGA→GGG) | rbbA ← | ribosome‑associated ATPase |
| RA | 3,728,118 | (C)8→9 | coding (1254/1455 nt) | xylB ← | xylulokinase |
| RA | 3,735,163 | C→T | A62V (GCC→GTC) | xylR → | DNA‑binding transcriptional dual regulator XylR |
| 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 | 3,863,090 | T→C | T172A (ACG→GCG) | glvC ← | putative PTS enzyme II component GlvC |
| RA | 3,905,198 | T→C | T134A (ACG→GCG) | bglF ← | beta‑glucoside specific PTS enzyme II/BglG kinase/BglG phosphatase |
| RA | 4,027,915 | C→T | P286P (CCG→CCA) | fadA ← | 3‑ketoacyl‑CoA thiolase |
| RA | 4,034,008 | T→C | C288C (TGT→TGC) | trkH → | K(+) transporter TrkH |
| RA | 4,266,164 | A→G | H128R (CAC→CGC) | alr → | alanine racemase 1 |
| RA | 4,287,743 | C→T | intergenic (‑372/‑21) | acs ← / → nrfA | acetyl‑CoA synthetase (AMP‑forming)/cytochrome c552 nitrite reductase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,466,452 | A→G | G265G (GGT→GGC) | treR ← | DNA‑binding transcriptional repressor TreR |
| RA | 4,554,262 | C→T | A454A (GCC→GCT) | uxuB → | D‑mannonate oxidoreductase |
| RA | 4,621,250 | A→G | D123G (GAC→GGC) | deoD → | purine nucleoside phosphorylase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 731133–731205 | 731290 | 86–158 | 24 [21] | [21] 22 | rhsC | rhs element protein RhsC |
| * | * | ÷ | NC_000913 | 731636–731710 | 732194–731990 | 281–559 | 24 [18] | [21] 23 | rhsC | rhs element protein RhsC |
| * | * | ÷ | NC_000913 | 732300–732457 | 733198–733065 | 609–899 | 22 [21] | [18] 24 | rhsC | rhs element protein RhsC |
| * | * | ÷ | NC_000913 | 1428235–1428306 | 1428456–1428330 | 25–222 | 24 [19] | [20] 23 | insH‑5 | Rac prophage; IS5 transposase and trans‑activator |
| * | * | ÷ | NC_000913 | 1431858 | 1432549–1432274 | 417–692 | 24 [21] | [20] 22 | [stfR]–[tfaR] | [stfR],[tfaR] |
| * | * | ÷ | NC_000913 | 1633048–1633221 | 1634546–1633925 | 705–1499 | 22 [20] | [21] 22 | ydfK–[tfaQ] | ydfK,pinQ,[tfaQ] |
| * | * | ÷ | NC_000913 | 3423755–3424234 | 3424531–3424238 | 5–777 | 26 [21] | [21] 22 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3944156–3945566 | 3945788–3945569 | 4–1633 | 23 [21] | [20] 26 | rrlC | 23S ribosomal RNA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 375001 = | NA (NA) | 27 (0.460) | 16/216 | 2.4 | NA | noncoding (17/36 nt) | other | REP31b |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | = 1207805 | 99 (1.330) | 20 (0.300) | 17/244 | 2.6 | 20.2% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 71 (1.080) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 51 (0.700) | 43/268 | 0.5 | 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 = | 122 (1.640) | 97 (1.310) | 57/274 | 0.2 | 61.0% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 3 (0.040) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 66 (0.890) | 47/276 | 0.4 | 94.3% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 4 (0.050) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||