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 | 1,152 | (C)5→6 | coding (816/2463 nt) | thrA → | fused aspartate kinase/homoserine dehydrogenase 1 |
RA | 9,074 | C→T | S279S (TCC→TCT) | talB → | transaldolase B |
RA | 45,294 | A→G | N372S (AAC→AGC) | fixC → | putative oxidoreductase FixC |
RA | 63,625 | G→A | P719L (CCC→CTC) | polB ← | DNA polymerase II |
RA | 126,807 | T→C | R371R (CGT→CGC) | aceF → | pyruvate dehydrogenase, E2 subunit |
RA | 136,457 | (T)8→9 | coding (8/867 nt) | speE ← | spermidine synthase |
RA | 137,887 | A→G | K269E (AAG→GAG) | cueO → | cuprous oxidase/multicopper oxidase with role in copper homeostasis |
RA | 140,172 | C→T | V352I (GTT→ATT) | gcd ← | quinoprotein glucose dehydrogenase |
RA | 150,781 | (A)6→5 | coding (173/1239 nt) | yadC ← | fimbrial tip‑adhesin YadC |
RA | 244,714 | Δ1 bp | coding (388/768 nt) | yafJ → | putative amidotransferase |
MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
RA | 280,348 | A→G | intergenic (‑473/+37) | insA‑2 ← / ← yagB | IS1 protein InsA/orphan antitoxin YagB |
RA | 308,344 | A→G | V330A (GTG→GCG) | ecpC ← | putative fimbrial usher protein EcpC |
RA | 312,523 | (C)5→6 | coding (255/264 nt) | ykgM ← | putative ribosomal protein |
RA | 341,200 | A→G | T26A (ACC→GCC) | yahJ → | putative deaminase with metallo‑dependent hydrolase domain |
RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
RA | 413,307 | T→C | D816G (GAC→GGC) | sbcC ← | ATP dependent, structure specific DNA nuclease ‑ SbcC subunit |
RA | 432,609 | A→G | G81G (GGT→GGC) | yajI ← | putative lipoprotein YajI |
RA | 437,593 | A→G | S181S (AGT→AGC) | yajO ← | 1‑deoxyxylulose‑5‑phosphate synthase YajO |
RA | 446,852 | A→G | V285A (GTA→GCA) | cyoE ← | heme O synthase |
RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
RA | 597,709 | T→C | S77S (AGT→AGC) | cusB → | copper/silver export system membrane fusion protein |
RA | 640,268 | G→A | P172P (CCG→CCA) | ahpF → | alkyl hydroperoxide reductase, AhpF component |
RA | 734,601 | C→T | pseudogene (382/1434 nt) | ybfO → | conserved protein, rhs‑like YbfO |
RA | 742,172 | A→G | Y129H (TAT→CAT) | dtpD ← | dipeptide:H(+) symporter DtpD |
RA | 750,625 | T→C | T515T (ACA→ACG) | ybgQ ← | putative fimbrial usher protein YbgQ |
RA | 808,482 | G→T | A259D (GCC→GAC) | bioA ← | adenosylmethionine‑8‑amino‑7‑oxononanoate aminotransferase |
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 | 955,295 | A→G | R446R (CGT→CGC) | ycaO ← | ribosomal protein S12 methylthiotransferase accessory factor YcaO |
RA | 1,004,160 | (G)7→8 | coding (214/711 nt) | ycbF → | putative fimbrial chaperone YcbF |
RA | 1,005,368 | C→T | Q201* (CAA→TAA) | pyrD → | dihydroorotate dehydrogenase, type 2 |
RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
RA | 1,013,628 | T→C | S124P (TCT→CCT) | pqiB → | intermembrane transport protein PqiB |
RA | 1,023,381 | T→C | D168G (GAC→GGC) | yccS ← | putative transporter YccS |
RA | 1,073,232 | A→G | F260F (TTT→TTC) | rutA ← | pyrimidine oxygenase |
RA | 1,134,819 | A→G | T31A (ACT→GCT) | flgG → | flagellar basal‑body rod protein FlgG |
RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
RA | 1,157,814 | (C)6→7 | intergenic (+240/‑55) | ycfH → / → ptsG | putative metal‑dependent hydrolase YcfH/glucose‑specific PTS enzyme IIBC component |
RA | 1,167,064 | T→C | V327A (GTT→GCT) | ndh → | NADH:quinone oxidoreductase II |
RA | 1,187,117 | A→G | intergenic (+47/+2) | pepT → / ← roxA | peptidase T/ribosomal protein‑arginine oxygenase |
RA | 1,193,012 | A→G | G254G (GGT→GGC) | mnmA ← | tRNA‑specific 2‑thiouridylase |
RA | 1,206,210 | T→C | pseudogene (80/792 nt) | jayE → | e14 prophage; putative protein JayE |
RA | 1,206,379 | C→T | pseudogene (249/792 nt) | jayE → | e14 prophage; putative protein JayE |
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 | 1,258,763 | A→G | intergenic (‑250/‑28) | pth ← / → ychH | peptidyl‑tRNA hydrolase/stress‑induced protein |
RA | 1,289,676 | A→G | A144A (GCA→GCG) | rssA → | putative patatin‑like phospholipase RssA |
MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
RA | 1,303,471 | T→C | R191R (CGT→CGC) | oppB → | murein tripeptide ABC transporter/oligopeptide ABC transporter inner membrane subunit OppB |
RA | 1,321,873 | C→T | E358E (GAG→GAA) | trpE ← | anthranilate synthase subunit TrpE |
RA | 1,325,794 | A→G | Q350R (CAG→CGG) | yciQ → | DUF2207 domain‑containing protein YciQ |
JC | 1,351,196 | (G)7→10 | intergenic (‑157/+211) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase/DUF559 domain‑containing protein YcjD |
RA | 1,371,015 | T→C | V267A (GTG→GCG) | ycjM → | glucosylglycerate phosphorylase |
RA | 1,429,354 | A→G | A102A (GCA→GCG) | stfR → | Rac prophage; putative membrane protein |
RA | 1,433,359 | T→C | T106A (ACC→GCC) | pinR ← | Rac prophage; putative site‑specific recombinase |
RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
RA | 1,551,142 | C→A | L228M (CTG→ATG) | fdnH → | formate dehydrogenase N subunit beta |
RA | 1,596,491 | A→G | pseudogene (1596/5422 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 | 1,745,969 | T→C | K53K (AAA→AAG) | ydhQ ← | adhesin‑like autotransporter YdhQ |
RA | 1,782,378 | C→A | A328A (GCC→GCA) | ydiS → | putative oxidoreductase with FAD/NAD(P)‑binding domain |
RA | 1,791,142 | T→C | T35A (ACC→GCC) | ydiU ← | UPF0061 family protein YdiU |
RA | 1,816,628 | T→C | S170G (AGC→GGC) | chbG ← | chitin disaccharide deacetylase |
RA | 1,837,283 | G→A | L24L (CTG→CTA) | ynjC → | putative ABC transporter membrane subunit YnjC |
RA | 1,845,694 | A→G | C423R (TGT→CGT) | topB ← | DNA topoisomerase III |
RA | 1,851,894 | (C)5→6 | coding (8/642 nt) | pncA → | nicotinamidase |
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 | 1,883,644 | A→G | T153A (ACC→GCC) | yeaV → | putative transporter YeaV |
RA | 1,893,022 | A→G | S72P (TCA→CCA) | yoaA ← | putative 5' to 3' DNA helicase implicated in DNA repair |
RA | 1,900,304 | T→C | T428A (ACG→GCG) | yoaE ← | putative inner membrane protein |
RA | 1,915,005 | T→C | H177R (CAC→CGC) | proQ ← | RNA chaperone ProQ |
RA | 1,918,762 | T→C | V418A (GTA→GCA) | yebT → | intermembrane transport protein YebT |
RA | 1,923,946 | (G)6→7 | coding (646/873 nt) | yebZ ← | putative inner membrane protein |
RA | 1,927,241 | (C)6→7 | coding (1599/2061 nt) | ptrB ← | oligopeptidase B |
RA | 1,971,513 | Δ1 bp | coding (1179/1662 nt) | tar ← | methyl‑accepting chemotaxis protein Tar |
RA | 1,975,369 | T→C | Q296R (CAG→CGG) | motB ← | motility protein B |
MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
RA | 1,996,183 | T→C | N217S (AAC→AGC) | sdiA ← | DNA‑binding transcriptional dual regulator SdiA |
RA | 2,025,603 | (C)5→6 | coding (93/816 nt) | yedP → | putative mannosyl‑3‑phosphoglycerate phosphatase |
RA | 2,052,343 | (T)6→7 | pseudogene (986/1053 nt) | yeeL ← | putative glycosyltransferase, N‑terminal fragment |
RA | 2,055,493 | T→C | Y145H (TAC→CAC) | amn → | AMP nucleosidase |
RA | 2,134,004 | A→G | V550A (GTG→GCG) | wzc ← | protein‑tyrosine kinase Wzc |
RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
RA | 2,183,854 | T→C | A221A (GCA→GCG) | thiD ← | bifunctional hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase |
RA | 2,357,116 | C→T | S71S (AGC→AGT) | rpnE → | inactive recombination‑promoting nuclease‑like protein RpnE |
RA | 2,376,205 | T→C | V205V (GTA→GTG) | menB ← | 1,4‑dihydroxy‑2‑naphthoyl‑CoA synthase |
RA | 2,384,744 | T→C | I327V (ATT→GTT) | yfbK ← | IPR002035/DUF3520 domain‑containing protein YfbK |
RA | 2,411,066 | A→G | V96A (GTT→GCT) | yfbS ← | putative transporter YfbS |
RA | 2,430,853 | G→A | intergenic (‑90/+169) | cvpA ← / ← dedD | colicin V production protein/cell division protein DedD |
RA | 2,438,498 | G→A | T183T (ACG→ACA) | flk → | putative flagella assembly protein |
RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
RA | 2,464,616 | T→C | H131R (CAC→CGC) | mlaA ← | intermembrane phospholipid transport system ‑ outer membrane lipoprotein MlaA |
RA | 2,481,946 | T→C | A77A (GCA→GCG) | emrY ← | tripartite efflux pump membrane subunit EmrY |
RA | 2,505,468 | A→G | L27P (CTG→CCG) | ypdE ← | broad‑specificity exoaminopeptidase |
RA | 2,517,170 | T→C | A221A (GCA→GCG) | pdeA ← | putative c‑di‑GMP phosphodiesterase PdeA |
RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
RA | 2,532,530 | T→C | V41A (GTT→GCT) | cysK → | O‑acetylserine sulfhydrylase A |
RA | 2,564,299 | T→C | V107A (GTC→GCC) | yffR → | CPZ‑55 prophage; uncharacterized protein YffR |
RA | 2,571,410 | G→A | G114G (GGC→GGT) | eutE ← | putative aldehyde dehydrogenase, ethanolamine utilization protein |
RA | 2,608,802 | T→C | S106P (TCA→CCA) | hyfG → | hydrogenase 4 catalytic subunit HyfG |
RA | 2,653,842 | T→C | intergenic (+503/‑13) | sseA → / → ryfA | 3‑mercaptopyruvate sulfurtransferase/small regulatory RNA RyfA |
RA | 2,669,673 | T→C | A214A (GCT→GCC) | hcaE → | putative 3‑phenylpropionate/cinnamate dioxygenase subunit alpha |
RA | 2,780,793 | G→A | A645V (GCC→GTC) | ypjA ← | adhesin‑like autotransporter YpjA |
RA | 2,810,502 | T→C | A53A (GCT→GCC) | ygaH → | L‑valine exporter subunit YgaH |
RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
RA | 2,830,031 | (T)7→6 | coding (219/966 nt) | gutQ → | D‑arabinose 5‑phosphate isomerase GutQ |
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 | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
RA | 3,073,340 | (T)6→7 | coding (352/1020 nt) | epd ← | D‑erythrose‑4‑phosphate dehydrogenase |
RA | 3,079,242 | A→G | V30A (GTA→GCA) | cmtB ← | mannitol‑specific PTS enzyme IIA component CmtB |
RA | 3,102,340 | (C)6→5 | coding (513/720 nt) | trmI ← | tRNA m(7)G46 methyltransferase |
RA | 3,125,139 | T→C | K107K (AAA→AAG) | glcF ← | glycolate dehydrogenase, putative iron‑sulfur subunit |
RA | 3,128,950 | A→C | T227P (ACC→CCC) | glcC → | DNA‑binding transcriptional dual regulator GlcC |
RA | 3,173,233 | T→C | V31A (GTA→GCA) | ygiN → | putative quinol monooxygenase YgiN |
RA | 3,194,156 | A→G | A431A (GCA→GCG) | yqiK → | protein YqiK |
RA | 3,285,180 | (G)5→6 | coding (496/804 nt) | agaC → | galactosamine‑specific PTS enzyme IIC component |
RA | 3,299,195 | C→T | G74G (GGC→GGT) | yhbO → | protein/nucleic acid deglycase 2 |
RA | 3,325,154 | T→C | A594A (GCA→GCG) | ftsH ← | ATP‑dependent zinc metalloprotease FtsH |
RA | 3,345,084 | A→G | Y123C (TAC→TGC) | rpoN → | RNA polymerase, sigma 54 (sigma N) factor |
RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
RA | 3,356,124 | A→G | E467G (GAG→GGG) | gltB → | glutamate synthase subunit GltB |
RA | 3,377,373 | A→G | G16G (GGT→GGC) | sspA ← | stringent starvation protein A |
RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
RA | 3,390,151 | G→A | R211H (CGC→CAC) | aaeR → | LysR‑type transcriptional regulator AaeR |
RA | 3,391,872 | G→A | R53C (CGC→TGC) | tldD ← | metalloprotease TldD |
RA | 3,422,311 | T→C | G329G (GGT→GGC) | yhdY → | putative ABC transporter membrane subunit YhdY |
RA | 3,507,394 | T→C | E103G (GAG→GGG) | yhfU ← | DUF2620 domain‑containing protein YhfU |
RA | 3,559,578 | A→G | E437E (GAA→GAG) | rtcR → | DNA‑binding transcriptional activator RtcR |
RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
RA | 3,719,092 | T→C | intergenic (‑48/‑386) | yiaF ← / → yiaG | DUF3053 domain‑containing protein YiaF/putative DNA‑binding transcriptional regulator YiaG |
RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
RA | 3,846,225 | A→G | W315R (TGG→CGG) | uhpT ← | hexose‑6‑phosphate:phosphate antiporter |
RA | 3,849,980 | G→A | L53L (CTG→TTG) | uhpB ← | sensory histidine kinase UhpB |
RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
RA | 3,913,854 | C→T | W449* (TGG→TGA) | glmU ← | fused N‑acetylglucosamine‑1‑phosphate uridyltransferase and glucosamine‑1‑phosphate acetyltransferase |
RA | 3,917,026 | T→C | Y117C (TAC→TGC) | atpD ← | ATP synthase F1 complex subunit beta |
RA | 3,920,989 | A→G | A67A (GCT→GCC) | atpE ← | ATP synthase Fo complex subunit c |
RA | 3,932,473 | A→G | A386A (GCA→GCG) | kup → | K(+):H(+) symporter Kup |
RA | 3,982,684 | (C)8→9 | noncoding (79/87 nt) | leuT → | tRNA‑Leu |
RA | 4,068,294 | A→G | V328A (GTG→GCG) | yihQ ← | sulfoquinovosidase |
RA | 4,269,672 | (A)7→8 | coding (259/714 nt) | aphA → | acid phosphatase/phosphotransferase |
RA | 4,279,976 | A→G | intergenic (+148/‑4) | ghxP → / → yjcE | guanine/hypoxanthine transporter GhxP/putative transporter YjcE |
RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
RA | 4,340,238 | (T)5→4 | coding (284/2268 nt) | adiA ← | arginine decarboxylase, degradative |
RA | 4,424,836 | G→A | intergenic (‑45/‑282) | yjfY ← / → rpsF | DUF1471 domain‑containing protein YjfY/30S ribosomal subunit protein S6 |
RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
RA | 4,467,176 | A→G | V24A (GTG→GCG) | treR ← | DNA‑binding transcriptional repressor TreR |
RA | 4,480,758 | T→C | G343G (GGT→GGC) | yjgN → | conserved inner membrane protein YjgN |
RA | 4,486,422 | T→C | F69L (TTC→CTC) | lptF → | lipopolysaccharide transport system protein LptF |
RA | 4,543,321 | A→G | G69G (GGA→GGG) | fimA → | type 1 fimbriae major subunit |
RA | 4,556,769 | (T)9→8 | coding (116/144 nt) | ytiD → | protein YtiD |
RA | 4,558,057 | A→T | I78N (ATC→AAC) | hypT ← | DNA‑binding transcriptional dual regulator HypT |
RA | 4,606,094 | (G)8→9 | noncoding (72/87 nt) | leuV ← | tRNA‑Leu |
RA | 4,606,215 | (G)8→9 | noncoding (72/87 nt) | leuP ← | tRNA‑Leu |
RA | 4,609,352 | A→G | intergenic (+29/‑62) | yjjG → / → prfC | pyrimidine nucleotidase/peptide chain release factor RF3 |
RA | 4,634,576 | T→C | G245G (GGA→GGG) | rob ← | DNA‑binding transcriptional dual regulator Rob |
Unassigned missing coverage evidence | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
seq id | start | end | size | ←reads | reads→ | gene | description | |||
* | * | ÷ | NC_000913 | 3423768–3424234 | 3424525–3424238 | 5–758 | 17 [12] | [12] 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 = | 10 (0.160) | 79 (1.400) | 45/244 | 0.1 | 90.4% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
? | NC_000913 | 1209619 = | 8 (0.140) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
* | ? | NC_000913 | = 1207805 | 10 (0.160) | 49 (0.870) | 37/244 | 0.4 | 85.3% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
? | NC_000913 | = 1209602 | 8 (0.140) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
* | ? | NC_000913 | 3363001 = | 100 (1.560) | 95 (1.500) | 58/274 | 0.1 | 65.7% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
? | NC_000913 | 3766087 = | 0 (0.000) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
* | ? | NC_000913 | = 3653230 | NA (NA) | 86 (1.350) | 54/276 | 0.1 | 97.7% | noncoding (1/1195 nt) | IS5 | repeat region |
? | NC_000913 | = 3766089 | 2 (0.030) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||
* | ? | NC_000913 | 4542682 = | 47 (0.740) | 19 (0.320) | 15/258 | 2.4 | 29.5% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
? | NC_000913 | 4542996 = | 47 (0.790) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
* | ? | NC_000913 | = 4542690 | 47 (0.740) | 22 (0.370) | 18/258 | 2.0 | 32.6% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
? | NC_000913 | = 4542986 | 47 (0.790) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |