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 | 37,214 | T→C | Y204C (TAC→TGC) | caiC ← | carnitine‑CoA ligase |
| RA | 47,100 | A→G | T432A (ACC→GCC) | yaaU → | putative transporter YaaU |
| RA | 58,993 | (A)7→8 | coding (520/651 nt) | yabP → | putative uncharacterized protein YabP |
| RA | 75,793 | A→G | C503R (TGC→CGC) | sgrR ← | DNA‑binding transcriptional dual regulator SgrR |
| RA | 121,360 | A→G | R64R (CGT→CGC) | aroP ← | aromatic amino acid:H(+) symporter AroP |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 290,698 | T→A | Q152L (CAG→CTG) | insB‑3 ← | IS1 protein InsB |
| RA | 308,602 | A→G | M244T (ATG→ACG) | ecpC ← | putative fimbrial usher protein EcpC |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 391,703 | (G)6→7 | pseudogene (1453/1458 nt) | yaiT → | putative autotransporter YaiT |
| RA | 476,217 | T→C | Y52C (TAC→TGC) | atl ← | DNA base‑flipping protein |
| RA | 482,655 | C→T | T583T (ACG→ACA) | acrB ← | multidrug efflux pump RND permease AcrB |
| RA | 489,576 | A→T | D1014V (GAT→GTT) | mscK → | potassium dependent, small conductance mechanosensitive channel |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 531,867 | A→G | Y119H (TAC→CAC) | allS ← | DNA‑binding transcriptional activator AllS |
| RA | 644,338 | A→G | G222G (GGT→GGC) | rna ← | RNase I |
| RA | 673,817 | C→T | A323T (GCA→ACA) | leuS ← | leucine‑‑tRNA ligase |
| RA | 791,748 | C→T | G103D (GGC→GAC) | galE ← | UDP‑glucose 4‑epimerase |
| RA | 824,192 | A→G | Y102Y (TAT→TAC) | ybhP ← | endonuclease/exonuclease/phosphatase domain‑containing protein YbhP |
| RA | 831,857 | A→G | Y329C (TAT→TGT) | rhlE → | ATP‑dependent RNA helicase RhlE |
| 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 | 967,145 | A→G | A175A (GCA→GCG) | msbA → | ATP‑binding lipopolysaccharide transport protein |
| RA | 983,465 | A→G | S131G (AGC→GGC) | ycbK → | DUF882 domain‑containing protein YcbK |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,013,073 | A→G | D358G (GAC→GGC) | pqiA → | intermembrane transport protein PqiA |
| RA | 1,052,050 | A→G | R68R (AGA→AGG) | ymcE → | protein YmcE |
| RA | 1,083,115 | C→T | F291F (TTC→TTT) | efeO → | ferrous iron transport system protein EfeO |
| RA | 1,093,358 | (G)6→7 | coding (483/1359 nt) | dgcT → | putative diguanylate cyclase DgcT |
| RA | 1,105,786 | A→G | intergenic (+61/‑34) | 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 | 1,210,492 | A→G | E49E (GAA→GAG) | mcrA → | e14 prophage; 5‑methylcytosine‑specific restriction enzyme McrA |
| 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 | 1,255,376 | C→T | V193I (GTC→ATC) | ycgV ← | putative autotransporter adhesin YcgV |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,354,110 | T→C | T137A (ACC→GCC) | sapC ← | putrescine ABC exporter membrane protein SapC |
| RA | 1,370,044 | (T)9→8 | intergenic (+41/‑172) | pspE → / → ycjM | thiosulfate sulfurtransferase PspE/glucosylglycerate phosphorylase |
| RA | 1,481,894 | Δ1 bp | coding (986/1293 nt) | ynbD → | putative phosphatase |
| RA | 1,521,796 | A→G | F424L (TTT→CTT) | yncD ← | putative TonB‑dependent outer membrane receptor |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,581,714 | T→C | T271A (ACA→GCA) | ydeN ← | putative sulfatase |
| RA | 1,597,074 | T→C | pseudogene (1013/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,609,419 | T→C | Y421C (TAT→TGT) | uxaB ← | tagaturonate reductase |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,684,740 | T→C | V161A (GTT→GCT) | tus → | DNA replication terminus site‑binding protein |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,772,250 | C→T | H394Y (CAC→TAC) | ydiM → | putative exporter YdiM |
| RA | 1,796,411 | T→C | T512A (ACC→GCC) | pheT ← | phenylalanine‑‑tRNA ligase subunit beta |
| RA | 1,811,947 | T→C | G338G (GGT→GGC) | tcyP → | cystine/sulfocysteine:cation symporter |
| RA | 1,812,360 | Δ1 bp | coding (773/804 nt) | ydjO ← | protein YdjO |
| 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 | 1,926,035 | T→C | L199S (TTA→TCA) | yobB → | putative carbon‑nitrogen hydrolase family protein YobB |
| RA | 1,943,238 | T→C | C193R (TGC→CGC) | znuC → | Zn(2(+)) ABC transporter ATP binding subunit |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,125,627 | T→C | A40A (GCA→GCG) | wcaI ← | putative colanic biosynthesis glycosyl transferase |
| RA | 2,154,161 | G→A | G49D (GGT→GAT) | mdtA → | multidrug efflux pump membrane fusion protein MdtA |
| RA | 2,167,173 | T→C | noncoding (60/87 nt) | cyaR → | small regulatory RNA CyaR |
| RA | 2,171,849 | A→G | V342A (GTG→GCG) | gatD ← | galactitol‑1‑phosphate 5‑dehydrogenase |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,193,588 | A→G | V194A (GTG→GCG) | mrp ← | P‑loop NTPase family protein |
| RA | 2,200,888 | A→T | I204F (ATC→TTC) | yehI → | DUF4132 domain‑containing protein YehI |
| RA | 2,204,803 | T→C | L70L (TTA→CTA) | yehL → | putative AAA(+) MoxR family ATPase YehL |
| RA | 2,229,288 | T→C | intergenic (+223/+150) | yohP → / ← dusC | putative membrane protein YohP/tRNA‑dihydrouridine(16) synthase |
| RA | 2,303,905 | (A)7→8 | coding (1/489 nt) | eco → | serine protease inhibitor ecotin |
| RA | 2,307,443 | T→C | Q391Q (CAA→CAG) | yojI ← | ABC transporter family protein/microcin J25 efflux protein |
| RA | 2,351,190 | G→A | G395G (GGC→GGT) | glpT ← | sn‑glycerol 3‑phosphate:phosphate antiporter |
| RA | 2,379,071 | Δ1 bp | coding (189/1671 nt) | menD ← | 2‑succinyl‑5‑enolpyruvyl‑6‑hydroxy‑3‑ cyclohexene‑1‑carboxylate synthase |
| RA | 2,384,097 | T→C | K542K (AAA→AAG) | yfbK ← | IPR002035/DUF3520 domain‑containing protein YfbK |
| RA | 2,399,877 | T→C | T97A (ACC→GCC) | nuoG ← | NADH:quinone oxidoreductase subunit G |
| RA | 2,427,677 | A→G | F39L (TTC→CTC) | argT ← | lysine/arginine/ornithine ABC transporter periplasmic binding protein |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,446,776 | G→A | A233V (GCG→GTG) | aroC ← | chorismate synthase |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,588,987 | G→A | A465T (GCC→ACC) | acrD → | multidrug efflux pump RND permease AcrD |
| RA | 2,603,299 | G→A | W494* (TGG→TGA) | hyfB → | hydrogenase 4 component B |
| RA | 2,610,630 | T→C | V156A (GTC→GCC) | hyfH → | hydrogenase 4 component H |
| RA | 2,687,920 | T→C | Y295C (TAC→TGC) | glrR ← | DNA‑binding transcriptional activator GlrR |
| RA | 2,783,959 | T→C | G157G (GGA→GGG) | ypjB ← | DUF5508 domain‑containing protein YpjB |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,814,020 | A→G | T469A (ACC→GCC) | emrB → | multidrug efflux pump membrane subunit EmrB |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,896,785 | Δ1 bp | coding (1086/1338 nt) | ygcS ← | putative transporter YgcS |
| RA | 2,928,232 | G→A | E2K (GAA→AAA) | sdaC → | serine:H(+) symporter SdaC |
| RA | 2,931,683 | T→C | V210A (GTT→GCT) | ygdG → | flap endonuclease |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 3,002,982 | T→C | D123D (GAT→GAC) | xdhB → | putative xanthine dehydrogenase FAD‑binding subunit XdhB |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,071,884 | T→C | T247A (ACC→GCC) | pgk ← | phosphoglycerate kinase |
| RA | 3,084,837 | T→C | T359A (ACC→GCC) | speA ← | arginine decarboxylase, biosynthetic |
| RA | 3,087,648 | A→G | T315A (ACT→GCT) | metK → | methionine adenosyltransferase |
| RA | 3,141,198 | T→C | Y30C (TAC→TGC) | hybD ← | putative hydrogenase 2 maturation protease |
| RA | 3,142,070 | G→A | A307V (GCG→GTG) | hybC ← | hydrogenase 2 large subunit |
| RA | 3,196,006 | G→A | P250S (CCA→TCA) | rfaE ← | fused heptose 7‑phosphate kinase/heptose 1‑phosphate adenyltransferase |
| RA | 3,266,649 | T→C | L139L (TTA→TTG) | tdcA ← | DNA‑binding transcriptional activator TdcA |
| RA | 3,270,044 | A→G | intergenic (+442/+172) | yhaC → / ← rnpB | uncharacterized protein YhaC/RNase P catalytic RNA component |
| RA | 3,281,898 | T→C | intergenic (+273/‑78) | agaA → / → agaS | putative truncated N‑acetylgalactosamine‑6‑phosphate deacetylase/putative galactosamine‑6‑phosphate deaminase/isomerase |
| RA | 3,304,459 | G→A | intergenic (+4/+114) | yhbW → / ← mtr | putative luciferase‑like monooxygenase/tryptophan:H(+) symporter Mtr |
| RA | 3,304,921 | G→A | L299L (CTC→CTT) | mtr ← | tryptophan:H(+) symporter Mtr |
| RA | 3,312,177 | G→A | R201C (CGC→TGC) | truB ← | tRNA pseudouridine(55) synthase |
| RA | 3,338,055 | T→C | D136G (GAC→GGC) | mlaD ← | intermembrane phospholipid transport system, substrate binding protein MlaD |
| 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 | 3,484,088 | (C)6→7 | coding (887/1023 nt) | yheT → | putative hydrolase YheT |
| RA | 3,497,200 | T→C | G66G (GGT→GGC) | nirC → | nitrite transporter NirC |
| RA | 3,518,866 | T→C | I67V (ATC→GTC) | aroK ← | shikimate kinase 1 |
| RA | 3,519,791 | C→T | E305K (GAG→AAG) | hofQ ← | DNA utilization protein HofQ |
| RA | 3,530,265 | A→G | K164K (AAA→AAG) | hslO → | molecular chaperone Hsp33 |
| RA | 3,536,836 | G→A | E9K (GAA→AAA) | greB → | transcription elongation factor GreB |
| RA | 3,542,066 | A→T | I554F (ATC→TTC) | feoB → | Fe(2(+)) transporter FeoB |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,589,296 | G→A | T244T (ACC→ACT) | ugpE ← | sn‑glycerol 3‑phosphate ABC transporter membrane subunit UgpE |
| RA | 3,622,422 | C→G | A1077A (GCC→GCG) | rhsB → | rhs element protein RhsB |
| RA | 3,622,659 | G→C | A1156A (GCG→GCC) | rhsB → | rhs element protein RhsB |
| RA | 3,622,662 | C→T | L1157L (CTC→CTT) | rhsB → | rhs element protein RhsB |
| RA | 3,622,670 | C→A | T1160K (ACG→AAG) | rhsB → | rhs element protein RhsB |
| RA | 3,639,042 | T→C | R467R (CGT→CGC) | pitA → | metal phosphate:H(+) symporter PitA |
| RA | 3,732,321 | T→C | S41P (TCT→CCT) | xylG → | xylose ABC transporter ATP binding subunit |
| RA | 3,771,923 | T→C | intergenic (‑179/‑358) | yibI ← / → mtlA | DUF3302 domain‑containing protein YibI/mannitol‑specific PTS enzyme IICBA component |
| RA | 3,786,481 | A→G | T408A (ACC→GCC) | gpmM → | 2,3‑bisphosphoglycerate‑independent phosphoglycerate mutase |
| RA | 3,786,865 | T→C | F10L (TTT→CTT) | envC → | murein hydrolase activator EnvC |
| RA | 3,793,227 | G→A | P153S (CCA→TCA) | htrL ← | protein HtrL |
| RA | 3,809,339 | T→C | V267A (GTA→GCA) | waaA → | KDO transferase |
| 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 | 3,910,873 | T→C | Y218C (TAT→TGT) | pstS ← | phosphate ABC transporter periplasmic binding protein |
| RA | 3,920,015 | (T)5→6 | coding (389/534 nt) | atpH ← | ATP synthase F1 complex subunit delta |
| RA | 3,961,221 | A→G | D182G (GAC→GGC) | rep → | ATP‑dependent DNA helicase Rep |
| RA | 3,962,223 | T→C | L516P (CTG→CCG) | rep → | ATP‑dependent DNA helicase Rep |
| RA | 3,967,714 | C→T | intergenic (+38/‑202) | rho → / → rfe | transcription termination factor Rho/UDP‑N‑acetylglucosamine‑‑undecaprenyl‑phosphate N‑acetylglucosaminephosphotransferase |
| RA | 4,031,693 | T→C | V178A (GTC→GCC) | pepQ → | Xaa‑Pro dipeptidase |
| RA | 4,158,511 | T→C | Y8H (TAC→CAC) | oxyR → | DNA‑binding transcriptional dual regulator OxyR |
| RA | 4,181,903 | T→C | I220T (ATC→ACC) | rpoB → | 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 | 4,338,117 | (A)8→7 | intergenic (‑188/+137) | adiY ← / ← adiA | DNA‑binding transcriptional activator AdiY/arginine decarboxylase, degradative |
| RA | 4,351,689 | A→G | intergenic (‑27/‑154) | dcuS ← / → yjdI | sensory histidine kinase DcuS/PF06902 family protein YjdI |
| RA | 4,363,460 | C→T | G528D (GGC→GAC) | dsbD ← | protein disulfide oxidoreductase ‑ DsbDreduced |
| RA | 4,391,975 | A→G | E124E (GAA→GAG) | orn → | oligoribonuclease |
| RA | 4,408,950 | A→G | D766G (GAC→GGC) | rnr → | RNase R |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,517,071 | A→G | V216A (GTG→GCG) | fecR ← | regulator for fec operon, periplasmic |
| RA | 4,604,172 | C→T | A232A (GCC→GCT) R5* (CGA→TGA) |
yjjQ → bglJ → |
DNA‑binding transcriptional repressor YjjQ DNA‑binding transcriptional regulator BglJ |
| RA | 4,606,215 | (G)8→9 | noncoding (72/87 nt) | leuP ← | tRNA‑Leu |
| RA | 4,638,743 | A→G | D189G (GAC→GGC) | creD → | putative inner membrane protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423766–3424234 | 3424525–3424238 | 5–760 | 21 [18] | [11] 21 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 4037962–4038687 | 4040493–4039392 | 706–2532 | 20 [19] | [19] 20 | [rrlA] | [rrlA] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 374921 = | NA (NA) | 40 (0.580) | 13/190 | 2.6 | NA | intergenic (+40/‑538) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377531 = | NA (NA) | intergenic (+220/+4) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 49 (0.720) | 16/190 | 2.1 | NA | noncoding (33/34 nt) | other | REP31a |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 375102 = | NA (NA) | 35 (0.450) | 16/216 | 2.5 | NA | noncoding (17/36 nt) | other | REP31d |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 1207790 = | 23 (0.230) | 92 (1.040) | 60/244 | 0.2 | 86.7% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 8 (0.090) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 23 (0.230) | 51 (0.580) | 42/244 | 0.6 | 78.3% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 8 (0.090) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 3363001 = | 137 (1.370) | 183 (1.850) | 87/274 | 0.0 | 72.5% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 3 (0.030) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 115 (1.150) | 59/276 | 0.3 | 96.6% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 4 (0.040) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||