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 | 104,040 | T→C | V20A (GTT→GCT) | ftsA → | cell division protein FtsA |
| RA | 133,173 | C→T | A520V (GCA→GTA) | acnB → | hypothetical protein |
| RA | 175,305 | (G)5→4 | coding (199/1422 nt) | clcA → | chloride:H(+) antiporter ClcA |
| RA | 179,819 | A→G | T195A (ACA→GCA) | dgt → | dGTP triphosphohydrolase |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 350,425 | A→G | K138K (AAA→AAG) | prpC → | 2‑methylcitrate synthase |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 399,946 | A→G | S326S (AGT→AGC) | ddlA ← | D‑alanine‑‑D‑alanine ligase A |
| RA | 438,348 | A→G | G610G (GGT→GGC) | dxs ← | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase |
| RA | 495,060 | T→C | intergenic (+50/‑60) | recR → / → htpG | DNA repair protein RecR/chaperone protein HtpG |
| RA | 501,785 | A→G | L485P (CTG→CCG) | ybaL ← | putative transporter YbaL |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 581,659 | T→C | pseudogene (306/309 nt) L42L (CTT→CTC) |
aaaD → tfaD → |
DLP12 prophage; protein AaaD DLP12 prophage; putative tail fiber assembly protein TfaD |
| RA | 601,940 | (A)6→7 | intergenic (+83/‑19) | cusA → / → pheP | copper/silver export system RND permease/phenylalanine:H(+) symporter PheP |
| RA | 616,051 | C→T | P632L (CCG→CTG) | entF → | apo‑serine activating enzyme |
| RA | 619,112 | G→T | A287S (GCG→TCG) | fepE → | polysaccharide co‑polymerase family protein FepE |
| RA | 632,017 | (G)7→8 | intergenic (+18/‑165) | cstA → / → ybdD | carbon starvation protein A/conserved protein YbdD |
| RA | 745,379 | A→G | Q72R (CAG→CGG) | pxpA → | 5‑oxoprolinase component A |
| RA | 863,752 | (A)6→7 | coding (111/663 nt) | fsaA → | fructose‑6‑phosphate aldolase 1 |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 904,019 | A→G | V150A (GTG→GCG) | ybjP ← | DUF3828 domain‑containing lipoprotein YbjP |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 961,603 | A→G | T135A (ACG→GCG) | cmk → | cytidylate kinase |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,024,403 | (T)7→8 | intergenic (‑55/‑68) | yccF ← / → helD | conserved inner membrane protein YccF/DNA helicase IV |
| RA | 1,056,632 | T→C | S124S (AGT→AGC) | torT → | periplasmic trimethylamine‑N‑oxide binding protein |
| RA | 1,097,793 | (T)7→8 | intergenic (‑141/‑93) | serX ← / → ghrA | tRNA‑Ser/glyoxylate/hydroxypyruvate reductase A |
| RA | 1,105,694 | A→G | K94R (AAG→AGG) | ymdA → | uncharacterized protein YmdA |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,160,930 | C→T | A208T (GCG→ACG) | fhuE ← | ferric coprogen/ferric rhodotorulic acid outer membrane transporter |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,279,520 | (T)7→6 | intergenic (+172/‑344) | narK → / → narG | nitrate:nitrite antiporter NarK/nitrate reductase A subunit alpha |
| RA | 1,283,138 | C→T | P1092L (CCG→CTG) | narG → | nitrate reductase A subunit alpha |
| RA | 1,464,089 | C→T | A184V (GCC→GTC) | paaX → | DNA‑binding transcriptional repressor PaaX |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,555,706 | (G)6→5 | intergenic (‑37/+120) | maeA ← / ← sra | malate dehydrogenase, NAD‑requiring/30S ribosomal subunit protein S22 |
| RA | 1,588,033 | C→T | V88V (GTG→GTA) | ydeR ← | putative fimbrial protein YdeR |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,647,558 | T→C | T27A (ACG→GCG) | ydfX ← | Qin prophage; uncharacterized protein YdfX |
| RA | 1,649,179 | G→A | intergenic (+138/‑203) | ydfC → / → dicF | Qin prophage; uncharacterized protein YdfC/Qin prophage; small regulatory RNA DicF |
| RA | 1,666,967 | C→T | A85T (GCG→ACG) | ynfK ← | putative dethiobiotin synthetase |
| 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 | 1,769,478 | (G)7→6 | coding (405/1113 nt) | ydiK → | putative transporter YdiK |
| RA | 1,810,965 | T→C | V11A (GTG→GCG) | tcyP → | cystine/sulfocysteine:cation symporter |
| RA | 1,828,362 | +A | coding (1373/1479 nt) | astD ← | aldehyde dehydrogenase |
| 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 | 1,922,069 | T→C | intergenic (+53/‑52) | yebV → / → yebW | protein YebV/protein YebW |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,010,317 | T→C | V166A (GTA→GCA) | yedK → | putative SOS response‑associated peptidase YedK |
| RA | 2,067,537 | T→C | intergenic (‑216/‑1098) | insH‑6 ← / → yoeA | CP4‑44 prophage; IS5 transposase and trans‑activator/CP4‑44 prophage; TonB‑dependent receptor plug domain‑containing protein YoeA |
| RA | 2,089,687 | C→T | A9A (GCG→GCA) | yefM ← | YefM antitoxin of the YoeB‑YefM toxin‑antitoxin pair and DNA binding transcriptional repressor |
| RA | 2,130,566 | T→C | T105A (ACA→GCA) | wcaD ← | putative colanic acid polymerase |
| RA | 2,143,684 | (G)6→7 | coding (419/3318 nt) | dgcE → | putative diguanylate cyclase DgcE |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,264,287 | T→C | V142A (GTG→GCG) | setB → | sugar exporter SetB |
| RA | 2,296,418 | T→C | T203A (ACC→GCC) | ccmB ← | heme trafficking system membrane protein CcmB |
| RA | 2,304,649 | C→T | intergenic (+256/+459) | eco → / ← mqo | serine protease inhibitor ecotin/malate:quinone oxidoreductase |
| RA | 2,389,171 | Δ1 bp | coding (56/849 nt) | yfbP → | uncharacterized protein YfbP |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,462,889 | (C)9→10 | intergenic (+243/‑123) | fadL → / → yfdF | long‑chain fatty acid outer membrane channel/bacteriophage T2 receptor/protein YfdF |
| RA | 2,473,806 | T→C | V68A (GTT→GCT) | yfdP → | CPS‑53 (KpLE1) prophage; protein YfdP |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,602,937 | (A)6→5 | coding (1120/2019 nt) | hyfB → | hydrogenase 4 component B |
| RA | 2,713,571 | T→C | Y226H (TAT→CAT) | srmB → | ATP‑dependent RNA helicase SrmB |
| RA | 2,717,821 | (C)5→6 | coding (708/1038 nt) | yfiF ← | putative methyltransferase |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,840,211 | T→C | C230R (TGC→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 | 2,925,525 | T→C | Y60H (TAT→CAT) | queF → | 7‑cyano‑7‑deazaguanine reductase |
| RA | 2,941,867 | T→C | Q234R (CAG→CGG) | gcvA ← | DNA‑binding transcriptional dual regulator GcvA |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,955,096 | T→C | E303G (GAA→GGA) | recB ← | exodeoxyribonuclease V subunit RecB |
| RA | 2,971,074 | T→C | F219L (TTC→CTC) | ygdQ → | UPF0053 inner membrane protein YgdQ |
| RA | 2,972,868 | T→C | E332G (GAG→GGG) | lplT ← | lysophospholipid transporter |
| RA | 2,973,932 | G→A | P695S (CCA→TCA) | aas ← | acyltransferase |
| RA | 3,017,986 | G→A | G643S (GGC→AGC) | ygfK → | putative oxidoreductase, Fe‑S subunit |
| RA | 3,027,822 | T→C | G234G (GGT→GGC) | ghxQ → | guanine/hypoxanthine transporter GhxQ |
| RA | 3,044,704 | A→G | D348G (GAC→GGC) | bglA → | 6‑phospho‑beta‑glucosidase A |
| RA | 3,048,737 | A→G | M102T (ATG→ACG) | gcvP ← | glycine decarboxylase |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,140,368 | T→C | V144V (GTA→GTG) | hybE ← | hydrogenase 2‑specific chaperone |
| RA | 3,187,731 | T→C | pseudogene (300/2434 nt) | yqiG → | putative outer membrane usher protein YqiG |
| RA | 3,194,558 | (A)5→6 | intergenic (+33/+163) | yqiK → / ← sibD | protein YqiK/small RNA SibD |
| RA | 3,209,866 | G→A | G226G (GGC→GGT) | tsaD ← | N(6)‑L‑threonylcarbamoyladenine synthase, TsaD subunit |
| RA | 3,221,129 | (T)6→7 | coding (119/333 nt) | ygjH ← | putative tRNA‑binding protein YgjH |
| RA | 3,222,236 | C→T | G257G (GGC→GGT) | ebgR → | DNA‑binding transcriptional repressor EbgR |
| RA | 3,231,341 | A→G | intergenic (+102/‑324) | ygjK → / → fadH | glycoside hydrolase/2,4‑dienoyl‑CoA reductase |
| RA | 3,236,458 | A→G | I167V (ATC→GTC) | ygjP → | putative metal‑dependent hydrolase |
| RA | 3,290,696 | A→G | N628S (AAC→AGC) | yraJ → | putative fimbrial usher protein YraJ |
| RA | 3,303,077 | T→C | C197R (TGC→CGC) | yhbV → | putative peptidase YhbV |
| RA | 3,346,067 | A→G | I451V (ATC→GTC) | rpoN → | RNA polymerase, sigma 54 (sigma N) factor |
| RA | 3,349,538 | T→C | H91R (CAC→CGC) | mtgA ← | peptidoglycan glycosyltransferase MtgA |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,359,761 | T→C | G188G (GGT→GGC) | gltD → | glutamate synthase subunit GltD |
| RA | 3,381,980 | T→C | V413A (GTG→GCG) | degQ → | periplasmic serine endoprotease |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,422,603 | T→C | R56R (CGT→CGC) | yhdZ → | putative ABC transporter ATP‑binding subunit YhdZ |
| RA | 3,489,210 | T→C | K324R (AAG→AGG) | argD ← | N‑acetylornithine aminotransferase/N‑succinyldiaminopimelate aminotransferase |
| RA | 3,498,721 | G→A | R298R (CGG→CGA) | cysG → | siroheme synthase |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,583,535 | T→C | V18A (GTG→GCG) | insA‑6 → | IS1 protein InsA |
| RA | 3,659,082 | (T)8→7 | noncoding (91/91 nt) | gadF → | small regulatory RNA GadF |
| RA | 3,728,118 | (C)8→7 | coding (1254/1455 nt) | xylB ← | xylulokinase |
| RA | 3,758,494 | C→T | A456A (GCG→GCA) | selB ← | selenocysteyl‑tRNA‑specific translation elongation factor |
| 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 | 3,891,717 | G→A | A35T (GCC→ACC) | mdtL → | efflux pump MdtL |
| RA | 3,961,495 | +T | coding (819/2022 nt) | rep → | ATP‑dependent DNA helicase Rep |
| RA | 4,180,017 | A→C | K8Q (AAA→CAA) | rplJ → | 50S ribosomal subunit protein L10 |
| RA | 4,250,104 | Δ1 bp | coding (551/921 nt) | malM → | maltose regulon periplasmic protein |
| RA | 4,255,616 | A→G | V284A (GTC→GCC) | plsB ← | glycerol‑3‑phosphate 1‑O‑acyltransferase |
| 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 | 4,499,799 | A→G | pseudogene (993/1199 nt) | yjgX ← | KpLE2 phage‑like element; putative phosphoethanolamine transferase YjgX, N‑terminal fragment |
| RA | 4,508,691 | (T)7→8 | intergenic (‑74/‑318) | insI‑3 ← / → insO | KpLE2 phage‑like element; IS30 transposase/KpLE2 phage‑like element; IS911B regulator fragment |
| RA | 4,587,133 | C→T | A62V (GCG→GTG) | mrr → | methylated adenine and cytosine restriction protein |
| RA | 4,606,330 | (G)8→9 | noncoding (72/87 nt) | leuQ ← | tRNA‑Leu |
| RA | 4,612,587 | C→T | G59G (GGC→GGT) | yjjU → | putative patatin‑like phospholipase YjjU |
| RA | 4,617,659 | G→A | G113S (GGT→AGT) | deoC → | deoxyribose‑phosphate aldolase |
| RA | 4,635,569 | C→T | P17S (CCA→TCA) | creA → | PF05981 family protein CreA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423791–3424234 | 3424523–3424238 | 5–733 | 19 [10] | [9] 16 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 22 (0.260) | 90 (1.220) | 50/244 | 0.2 | 82.4% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 19 (0.260) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 22 (0.260) | 51 (0.690) | 37/244 | 0.6 | 72.6% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 19 (0.260) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 66 (0.810) | 44/268 | 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 = | 106 (1.270) | 126 (1.520) | 66/274 | 0.1 | 70.2% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 2 (0.020) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 87 (1.040) | 57/276 | 0.2 | 97.8% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 2 (0.020) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||