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 | 8,322 | C→T | P29S (CCG→TCG) | talB → | transaldolase B |
| RA | 46,734 | C→T | P310S (CCA→TCA) | yaaU → | putative transporter YaaU |
| RA | 78,637 | A→G | A339A (GCA→GCG) | setA → | sugar exporter SetA |
| RA | 213,286 | A→G | N319S (AAC→AGC) | tilS → | tRNA(Ile)‑lysidine synthetase |
| RA | 236,613 | A→G | T183A (ACG→GCG) | dnaQ → | DNA polymerase III subunit epsilon |
| RA | 254,329 | A→G | V463A (GTT→GCT) | pepD ← | peptidase D |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 269,159 | C→T | intergenic (‑199/+130) | ykfA ← / ← perR | CP4‑6 prophage; putative GTP‑binding protein YkfA/putative transcriptional regulator PerR |
| RA | 308,054 | (C)7→8 | coding (1279/2526 nt) | ecpC ← | putative fimbrial usher protein EcpC |
| RA | 317,683 | (G)5→6 | intergenic (‑547/+43) | ykgA ← / ← rclC | putative DNA‑binding transcriptional regulator YkgA/reactive chlorine species resistance protein C |
| RA | 358,871 | C→T | Q25* (CAG→TAG) | cynT → | carbonic anhydrase 1 |
| RA | 375,928 | C→T | T157I (ACA→ATA) | mhpT → | 3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| RA | 380,021 | (G)10→8 | intergenic (‑140/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 407,368 | C→T | intergenic (+198/‑60) | yaiA → / → aroM | protein YaiA/protein AroM |
| RA | 455,159 | A→G | Q9Q (CAA→CAG) | tig → | trigger factor |
| RA | 455,857 | A→G | E242G (GAG→GGG) | tig → | trigger factor |
| RA | 517,217 | T→C | V212A (GTG→GCG) | fetB → | putative iron ABC exporter membrane subunit FetB |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 553,146 | A→G | intergenic (‑46/+72) | purE ← / ← lpxH | N(5)‑carboxyaminoimidazole ribonucleotide mutase/UDP‑2,3‑diacylglucosamine diphosphatase |
| RA | 564,993 | A→G | V329A (GTC→GCC) | intD ← | DLP12 prophage; putative integrase |
| RA | 713,628 | C→T | A24V (GCG→GTG) | pgm → | phosphoglucomutase |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 1,004,160 | (G)7→8 | coding (214/711 nt) | ycbF → | putative fimbrial chaperone YcbF |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,075,827 | A→G | V1019A (GTC→GCC) | putA ← | fused DNA‑binding transcriptional repressor/proline dehydrogenase/1‑pyrroline‑5‑carboxylate dehydrogenase PutA |
| RA | 1,100,871 | A→G | S272P (TCG→CCG) | csgG ← | curli secretion channel |
| RA | 1,105,737 | A→G | intergenic (+12/‑83) | ymdA → / → ymdB | uncharacterized protein YmdA/2'‑O‑acetyl‑ADP‑ribose deacetylase, regulator of RNase III activity |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,162,938 | A→G | S101G (AGC→GGC) | lpoB → | outer membrane lipoprotein ‑ activator of MrcB activity |
| RA | 1,175,955 | C→T | R177C (CGT→TGT) | lolC → | lipoprotein release complex ‑ inner membrane subunit |
| RA | 1,177,836 | T→C | S173P (TCG→CCG) | lolE → | lipoprotein release complex ‑ inner membrane subunit |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,227,995 | C→T | D105D (GAC→GAT) | ycgL → | PF05166 family protein YcgL |
| RA | 1,270,494 | +C | intergenic (+34/+255) | rdlC → / ← chaA | small regulatory antisense RNA RdlC/Na(+)/K(+):H(+) antiporter ChaA |
| RA | 1,296,985 | C→T | P379P (CCG→CCA) | adhE ← | aldehyde‑alcohol dehydrogenase |
| MC JC | 1,297,367 | (ACA)4→3 | coding (753‑755/2676 nt) | adhE ← | aldehyde‑alcohol dehydrogenase |
| RA | 1,336,633 | T→C | V268A (GTT→GCT) | acnA → | aconitate hydratase 1 |
| RA | 1,338,923 | C→T | E80K (GAG→AAG) | ribA ← | GTP cyclohydrolase 2 |
| RA | 1,351,196 | (G)7→8 | intergenic (‑157/+211) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase/DUF559 domain‑containing protein YcjD |
| RA | 1,398,452 | A→G | R57R (CGT→CGC) | uspE ← | universal stress protein with a role cellular motility |
| RA | 1,479,590 | A→G | A151A (GCA→GCG) | ynbC → | hydrolase/methyltransferase domain‑containing protein YnbC |
| RA | 1,502,847 | A→G | T131A (ACC→GCC) | ydcL → | DUF3313 domain‑containing lipoprotein YdcL |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,594,256 | (C)8→7 | 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 | 1,646,191 | A→G | T99A (ACC→GCC) | ydfV → | Qin prophage; protein YdfV |
| RA | 1,654,101 | T→C | E347E (GAA→GAG) | rspA ← | mandelate racemase/muconate lactonizing enzyme family protein RspA |
| RA | 1,662,154 | A→G | A533A (GCA→GCG) | ynfF → | putative selenate reductase YnfF |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,714,326 | (T)9→8 | intergenic (+55/‑51) | dtpA → / → gstA | dipeptide/tripeptide:H(+) symporter DtpA/glutathione S‑transferase GstA |
| RA | 1,719,230 | T→C | T125A (ACC→GCC) | anmK ← | anhydro‑N‑acetylmuramic acid kinase |
| RA | 1,720,436 | A→G | I130T (ATC→ACC) | slyA ← | DNA‑binding transcriptional dual regulator SlyA |
| RA | 1,758,523 | G→A | A68V (GCC→GTC) | ldtE ← | L,D‑transpeptidase LdtE |
| RA | 1,801,794 | T→C | E259E (GAA→GAG) | thrS ← | threonine‑‑tRNA ligase |
| RA | 1,834,839 | A→G | Y11C (TAC→TGC) | ydjZ → | DedA family protein YdjZ |
| 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 | 1,886,797 | T→C | V318A (GTG→GCG) | yeaX → | carnitine monooxygenase subunit YeaX |
| RA | 1,910,848 | G→A | L191L (CTG→CTA) | yebQ → | putative transporter YebQ |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,014,272 | T→C | R348R (CGT→CGC) | fliF → | flagellar basal‑body MS‑ring and collar protein |
| RA | 2,130,344 | (A)5→4 | coding (535/1218 nt) | wcaD ← | putative colanic acid polymerase |
| RA | 2,130,735 | T→C | E48E (GAA→GAG) | wcaD ← | putative colanic acid polymerase |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,338,438 | A→G | V328A (GTT→GCT) | gyrA ← | DNA gyrase subunit A |
| RA | 2,403,585 | T→C | L87L (TTA→TTG) | nuoC ← | NADH:quinone oxidoreductase subunit CD |
| RA | 2,417,868 | T→C | V263A (GTG→GCG) | yfcC → | putative transporter YfcC |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,471,844 | T→C | pseudogene (219/519 nt) | yfdL ← | CPS‑53 (KpLE1) prophage; putative uncharacterized protein YfdL |
| RA | 2,473,862 | T→C | Y87H (TAT→CAT) | yfdP → | CPS‑53 (KpLE1) prophage; protein YfdP |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,554,532 | (C)5→6 | coding (651/1053 nt) | eutR ← | putative AraC‑type transcriptional regulator EutR |
| RA | 2,585,544 | T→C | intergenic (‑19/‑187) | aegA ← / → narQ | putative oxidoreductase Fe‑S subunit AegA/sensory histidine kinase NarQ |
| RA | 2,602,017 | (C)7→8 | coding (200/2019 nt) | hyfB → | hydrogenase 4 component B |
| RA | 2,624,311 | T→C | V423A (GTG→GCG) | ppk → | polyphosphate kinase |
| RA | 2,644,370 | (G)5→6 | intergenic (‑87/+63) | rlmN ← / ← ndk | 23S rRNA m(2)A2503 methyltransferase/tRNA m(2)A37 methyltransferase/nucleoside diphosphate kinase |
| RA | 2,723,923 | A→G | P399P (CCA→CCG) | pssA → | phosphatidylserine synthase |
| RA | 2,745,237 | T→C | S35G (AGC→GGC) | trmD ← | tRNA m(1)G37 methyltransferase |
| RA | 2,764,538 | G→A | R206C (CGC→TGC) | abpA ← | CP4‑57 prophage; anti‑bacteriophage protein |
| 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 | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,821,424 | G→C | G196G (GGC→GGG) | alaS ← | alanine‑‑tRNA ligase/DNA‑binding transcriptional repressor |
| RA | 2,840,452 | A→G | H310R (CAC→CGC) | ascF → | beta‑glucoside specific PTS enzyme IIBC component |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,951,007 | G→A | A485A (GCC→GCT) | recD ← | exodeoxyribonuclease V subunit RecD |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,148,923 | T→C | S343P (TCT→CCT) | gpr → | L‑glyceraldehyde 3‑phosphate reductase |
| RA | 3,163,735 | T→C | S747G (AGC→GGC) | parC ← | DNA topoisomerase IV subunit A |
| RA | 3,168,226 | G→A | H7H (CAC→CAT) | mqsA ← | antitoxin of the MqsRA toxin‑antitoxin system/DNA‑binding transcriptional repressor MqsA |
| RA | 3,188,182 | A→G | pseudogene (751/2434 nt) | yqiG → | putative outer membrane usher protein YqiG |
| RA | 3,216,781 | G→A | M1M (ATG→ATA) † | nfeR → | DNA‑binding transcriptional repressor NfeR |
| RA | 3,249,080 | G→A | A38T (GCC→ACC) | yqjC → | DUF1090 domain‑containing protein YqjC |
| RA | 3,254,443 | T→C | V42A (GTG→GCG) | yhaK → | bicupin‑related protein |
| RA | 3,350,177 | A→C | F95V (TTT→GTT) | elbB ← | low activity glyoxalase ElbB |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,385,512 | T→C | intergenic (+339/‑26) | argR → / → yhcN | DNA‑binding transcriptional dual regulator ArgR/DUF1471 domain‑containing stress‑induced protein YhcN |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,403,790 | C→T | R103* (CGA→TGA) | yhdH → | acrylyl‑CoA reductase |
| RA | 3,405,687 | T→C | R84R (CGT→CGC) | accB → | biotin carboxyl carrier protein |
| RA | 3,421,409 | T→C | F29L (TTC→CTC) | yhdY → | putative ABC transporter membrane subunit YhdY |
| RA | 3,438,502 | T→C | N50D (AAC→GAC) | arfA ← | alternative ribosome‑rescue factor A |
| RA | 3,456,803 | (C)6→7 | coding (427/1953 nt) | gspD → | Type II secretion system protein GspD |
| RA | 3,468,938 | T→C | T306A (ACT→GCT) | chiA ← | endochitinase |
| RA | 3,492,018 | T→C | N94D (AAC→GAC) | ppiA ← | peptidyl‑prolyl cis‑trans isomerase A |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,579,158 | T→C | Y163C (TAC→TGC) | yhhW ← | quercetin 2,3‑dioxygenase |
| RA | 3,729,740 | T→C | V342V (GTA→GTG) | xylA ← | xylose isomerase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,847,452 | (C)5→4 | coding (1173/1320 nt) | uhpC ← | inner membrane protein sensing glucose‑6‑phosphate |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,885,773 | A→G | Y233C (TAC→TGC) | yidC → | membrane protein insertase YidC |
| RA | 3,922,931 | (A)7→6 | intergenic (‑491/+126) | atpI ← / ← rsmG | ATP synthase accessory factor/16S rRNA m(7)G527 methyltransferase |
| RA | 3,936,477 | A→G | N67S (AAC→AGC) | rbsB → | ribose ABC transporter periplasmic binding protein |
| RA | 3,948,369 | C→T | S95F (TCC→TTC) | maoP → | macrodomain Ori protein |
| RA | 4,060,280 | (T)9→8 | intergenic (+50/‑167) | bipA → / → yihL | ribosome‑dependent GTPase, ribosome assembly factor/putative transcriptional regulator YihL |
| RA | 4,069,827 | T→C | Y192C (TAT→TGT) | yihR ← | putative aldose 1‑epimerase YihR |
| RA | 4,147,556 | A→G | R254R (CGT→CGC) | yijO ← | putative DNA‑binding transcriptional regulator YijO |
| RA | 4,148,884 | T→C | D461G (GAC→GGC) | eptC ← | phosphoethanolamine transferase EptC |
| RA | 4,197,901 | A→G | Q62Q (CAA→CAG) | hemE → | uroporphyrinogen decarboxylase |
| RA | 4,237,668 | T→C | L12P (CTG→CCG) | yjbH → | YjbH family protein |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,357,077 | A→G | V514A (GTG→GCG) | cadA ← | lysine decarboxylase 1 |
| RA | 4,423,458 | G→A | G205R (GGG→AGG) | ulaE → | L‑ribulose‑5‑phosphate 3‑epimerase UlaE |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,448,473 | (G)5→6 | coding (27/252 nt) | chpS → | ChpS antitoxin of the ChpB‑ChpS toxin‑antitoxin system |
| RA | 4,464,536 | A→G | S58S (TCT→TCC) | treC ← | trehalose‑6‑phosphate hydrolase |
| RA | 4,472,706 | A→G | intergenic (‑173/+108) | pyrL ← / ← yjgH | pyrBI operon leader peptide/RutC family protein YjgH |
| RA | 4,482,676 | C→T | V388I (GTC→ATC) | valS ← | valine‑‑tRNA ligase |
| RA | 4,606,094 | (G)8→7 | noncoding (72/87 nt) | leuV ← | tRNA‑Leu |
| RA | 4,606,215 | (G)8→9 | noncoding (72/87 nt) | leuP ← | tRNA‑Leu |
| RA | 4,606,330 | (G)8→9 | noncoding (72/87 nt) | leuQ ← | tRNA‑Leu |
| RA | 4,621,600 | T→C | *240Q (TAA→CAA) | deoD → | purine nucleoside phosphorylase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1269464 | 1270441 | 978 | 13 [10] | [12] 14 | ldrB–[rdlC] | ldrB,rdlB,ldrC,[rdlC] |
| * | * | ÷ | NC_000913 | 3423784–3424233 | 3424528–3424238 | 6–745 | 14 [12] | [12] 14 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 4037529–4037833 | 4040483–4039392 | 1560–2955 | 13 [11] | [12] 13 | [rrlA] | [rrlA] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 30 (0.500) | 47 (0.880) | 39/242 | 0.2 | 68.4% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 17 (0.320) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 30 (0.500) | 25 (0.470) | 23/242 | 1.0 | 53.5% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 17 (0.320) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 53 (0.900) | 39/266 | 0.3 | 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 = | 95 (1.570) | 96 (1.600) | 57/272 | 0.1 | 66.6% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 2 (0.030) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 73 (1.210) | 52/274 | 0.1 | 92.4% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 6 (0.100) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | 4542682 = | 31 (0.510) | 18 (0.320) | 15/256 | 2.1 | 36.4% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 34 (0.600) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 31 (0.510) | 26 (0.460) | 21/256 | 1.3 | 45.2% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 34 (0.600) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||