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 | 48,498 | G→A | G244S (GGC→AGC) | kefC → | K(+) : H(+) antiporter KefC |
| RA | 66,691 | C→T | intergenic (‑141/+144) | araD ← / ← araA | L‑ribulose‑5‑phosphate 4‑epimerase AraD/L‑arabinose isomerase |
| RA | 75,380 | (C)5→4 | coding (101/984 nt) | thiB ← | thiamine ABC transporter periplasmic binding protein |
| RA | 77,407 | A→G | noncoding (41/227 nt) H7R (CAC→CGC) |
sgrS → sgrT → |
small regulatory RNA SgrS putative inhibitor of the PtsG glucose transporter |
| RA | 91,413 | A→G | M1M (ATG→GTG) † | ftsI → | peptidoglycan DD‑transpeptidase FtsI |
| RA | 117,102 | C→T | intergenic (‑3/+7) | hofB ← / ← ppdD | T2SSE family protein/prepilin peptidase‑dependent protein |
| RA | 181,141 | T→C | G86G (GGT→GGC) | degP → | periplasmic serine endoprotease DegP |
| RA | 257,594 | G→A | T356T (ACG→ACA) | frsA → | fermentation‑respiration switch protein |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 265,949 | T→G | K47Q (AAG→CAG) | ykfB ← | CP4‑6 prophage; protein YkfB |
| RA | 441,928 | A→G | Y127C (TAC→TGC) | thiI → | tRNA uridine 4‑sulfurtransferase |
| RA | 483,569 | C→T | A279T (GCA→ACA) | acrB ← | multidrug efflux pump RND permease AcrB |
| RA | 490,933 | A→G | T18A (ACG→GCG) | ybaN → | conserved inner membrane protein YbaN |
| RA | 504,205 | T→C | G164G (GGA→GGG) | fsr ← | fosmidomycin efflux pump |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 554,473 | C→T | intergenic (‑36/‑138) | ppiB ← / → cysS | peptidyl‑prolyl cis‑trans isomerase B/cysteine‑‑tRNA ligase |
| RA | 564,993 | A→G | V329A (GTC→GCC) | intD ← | DLP12 prophage; putative integrase |
| RA | 590,706 | C→T | L83L (CTG→CTA) | nfrA ← | bacteriophage N4 receptor, outer membrane protein |
| RA | 658,555 | G→A | pseudogene (525/788 nt) | ybeM → | deamidated glutathione amidase, N‑terminal fragment |
| RA | 732,957 | G→C | T1125T (ACG→ACC) | rhsC → | rhs element protein RhsC |
| RA | 732,962 | C→A | A1127E (GCG→GAG) | rhsC → | rhs element protein RhsC |
| RA | 735,912 | T→C | V88A (GTC→GCC) | ybfC → | uncharacterized protein YbfC |
| RA | 737,430 | T→A | pseudogene (531/1062 nt) | ybfL → | putative transposase YbfL |
| RA | 764,988 | G→A | G270D (GGC→GAC) | sucD → | succinyl‑CoA synthetase subunit alpha |
| RA | 783,455 | C→T | A97V (GCG→GTG) | pnuC → | nicotinamide riboside transporter |
| RA | 812,758 | A→G | I163M (ATA→ATG) | bioD → | dethiobiotin synthetase |
| RA | 868,422 | (C)8→9 | coding (903/1872 nt) | gsiA → | glutathione ABC transporter ATP binding subunit GsiA |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 909,821 | T→C | N410S (AAC→AGC) | poxB ← | pyruvate oxidase |
| RA | 915,074 | C→G | intergenic (‑217/+278) | lysO ← / ← aqpZ | L‑lysine exporter/water channel AqpZ |
| RA | 916,237 | A→G | intergenic (‑190/‑236) | aqpZ ← / → ybjD | water channel AqpZ/DUF2813 domain‑containing protein YbjD |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 1,000,902 | T→C | S563P (TCC→CCC) | elfC → | putative fimbrial usher protein ElfC |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,133,367 | C→T | S265F (TCC→TTC) | flgE → | flagellar hook protein FlgE |
| 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 | 1,224,623 | A→G | L247L (TTG→CTG) | minD ← | Z‑ring positioning protein MinD |
| RA | 1,279,364 | A→G | intergenic (+16/‑500) | narK → / → narG | nitrate:nitrite antiporter NarK/nitrate reductase A subunit alpha |
| RA | 1,370,044 | (T)9→8 | intergenic (+41/‑172) | pspE → / → ycjM | thiosulfate sulfurtransferase PspE/glucosylglycerate phosphorylase |
| RA | 1,385,729 | A→G | G73G (GGA→GGG) | ycjF → | conserved inner membrane protein YcjF |
| RA | 1,464,788 | T→C | G106G (GGT→GGC) | paaY → | 2‑hydroxycyclohepta‑1,4,6‑triene‑1‑carboxyl‑CoA thioesterase |
| RA | 1,501,680 | G→A | G40D (GGC→GAC) | tehB → | tellurite methyltransferase |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,544,435 | T→C | pseudogene (285/336 nt) | yddJ ← | uncharacterized protein YddJ |
| RA | 1,569,408 | C→T | G361D (GGC→GAC) | gadC ← | L‑glutamate:4‑aminobutyrate antiporter |
| RA | 1,594,132 | (C)8→9 | pseudogene (3955/5422 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 | 1,743,004 | T→C | D80G (GAT→GGT) | ribC ← | riboflavin synthase |
| RA | 1,762,453 | T→C | L20L (TTA→TTG) | sufC ← | Fe‑S cluster scaffold complex subunit SufC |
| RA | 1,779,230 | Δ1 bp | coding (72/912 nt) | ydiP ← | putative DNA‑binding transcriptional regulator YdiP |
| RA | 1,814,080 | C→T | R72C (CGC→TGC) | katE → | catalase II |
| RA | 1,818,822 | G→A | A209V (GCG→GTG) | chbR ← | DNA‑binding transcriptional dual regulator ChbR |
| RA | 1,833,210 | (C)5→6 | coding (783/807 nt) | xthA → | exodeoxyribonuclease III |
| RA | 1,865,871 | A→G | L201P (CTG→CCG) | mipA ← | scaffolding protein that interacts with murein polymerase and murein hydrolase |
| 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 | 1,948,205 | T→C | E143G (GAA→GGA) | nudB ← | dihydroneopterin triphosphate diphosphatase |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,036,963 | (T)5→4 | coding (1190/1359 nt) | hprS ← | sensory histidine kinase HprS |
| RA | 2,073,106 | A→G | D523G (GAC→GGC) | flu → | CP4‑44 prophage; self recognizing antigen 43 (Ag43) autotransporter |
| RA | 2,093,363 | T→C | R322R (CGT→CGC) | hisC → | histidinol‑phosphate aminotransferase |
| RA | 2,116,428 | (T)6→7 | coding (700/1221 nt) | wcaL ← | putative colanic biosynthesis glycosyl transferase |
| RA | 2,163,776 | T→C | S301P (TCT→CCT) | baeS → | sensory histidine kinase BaeS |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,235,274 | A→G | K4E (AAA→GAA) | preA → | NAD‑dependent dihydropyrimidine dehydrogenase subunit PreA |
| RA | 2,321,743 | T→C | G567G (GGT→GGC) | atoS → | sensory histidine kinase AtoS |
| RA | 2,389,259 | T→C | G48G (GGT→GGC) | yfbP → | uncharacterized protein YfbP |
| RA | 2,429,902 | (T)6→7 | coding (337/1518 nt) | purF ← | amidophosphoribosyltransferase |
| RA | 2,440,577 | A→G | A343A (GCT→GCC) | fabB ← | beta‑ketoacyl‑[acyl carrier protein] synthase I |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,484,483 | T→C | V37A (GTC→GCC) | evgS → | sensory histidine kinase EvgS |
| RA | 2,484,897 | (C)6→7 | coding (524/3594 nt) | evgS → | sensory histidine kinase EvgS |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,595,175 | A→G | S229P (TCA→CCA) | tmcA ← | tRNA(Met) cytidine acetyltransferase |
| RA | 2,637,981 | G→A | G224G (GGC→GGT) | bamB ← | outer membrane protein assembly factor BamB |
| RA | 2,725,530 | A→G | F73L (TTC→CTC) | kgtP ← | alpha‑ketoglutarate:H(+) symporter |
| RA | 2,769,953 | A→G | H84R (CAC→CGC) | yfjR → | CP4‑57 prophage; putative DNA‑binding transcriptional regulator |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,836,093 | T→C | T445A (ACC→GCC) | hypF ← | carbamoyltransferase HypF |
| RA | 2,847,717 | C→T | A509T (GCC→ACC) | hycC ← | formate hydrogenlyase subunit HycC |
| RA | 2,855,313 | A→G | T326A (ACC→GCC) | fhlA → | DNA‑binding transcriptional activator FhlA |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,878,707 | T→C | G49G (GGA→GGG) | cas2 ← | CRISPR‑associated endoribonuclease Cas2 |
| RA | 2,931,420 | G→A | T122T (ACG→ACA) | ygdG → | flap endonuclease |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 3,039,943 | T→C | V30A (GTG→GCG) | fldB → | flavodoxin 2 |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,092,075 | G→A | W66* (TGG→TGA) | gshB → | glutathione synthetase |
| RA | 3,101,039 | (C)7→9 | coding (585/720 nt) | yggN ← | putative EcfF |
| RA | 3,102,219 | C→T | A212T (GCA→ACA) | trmI ← | tRNA m(7)G46 methyltransferase |
| RA | 3,114,688 | (C)5→6 | coding (4425/4563 nt) | yghJ ← | putative lipoprotein YghJ |
| RA | 3,127,002 | C→T | A340A (GCG→GCA) | glcD ← | glycolate dehydrogenase, putative FAD‑linked subunit |
| RA | 3,137,780 | T→A | D248V (GAT→GTT) | gss ← | fused glutathionylspermidine amidase/glutathionylspermidine synthetase |
| RA | 3,161,091 | T→C | Y19C (TAC→TGC) | ygiQ ← | radical SAM superfamily protein YgiQ |
| RA | 3,193,821 | A→T | I320F (ATC→TTC) | yqiK → | protein YqiK |
| RA | 3,210,638 | T→C | intergenic (‑95/‑143) | tsaD ← / → rpsU | N(6)‑L‑threonylcarbamoyladenine synthase, TsaD subunit/30S ribosomal subunit protein S21 |
| RA | 3,211,354 | T→C | V83A (GTC→GCC) | dnaG → | DNA primase |
| RA | 3,240,984 | (G)7→9 | coding (1041/1245 nt) | sstT → | serine/threonine:Na(+) symporter |
| RA | 3,247,385 | Δ1 bp | coding (734/777 nt) | exuR → | DNA‑binding transcriptional repressor ExuR |
| RA | 3,304,813 | (C)7→8 | coding (1005/1245 nt) | mtr ← | tryptophan:H(+) symporter Mtr |
| RA | 3,335,960 | T→C | T179A (ACC→GCC) | murA ← | UDP‑N‑acetylglucosamine 1‑carboxyvinyltransferase |
| RA | 3,338,527 | T→C | H241R (CAC→CGC) | mlaE ← | intermembrane phospholipid transport system, integral membrane subunit MlaE |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,371,768 | A→G | S269S (AGT→AGC) | nanT ← | N‑acetylneuraminate:H(+) symporter |
| RA | 3,387,870 | T→C | T107A (ACC→GCC) | aaeB ← | aromatic carboxylic acid efflux pump subunit AaeB |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,399,266 | A→G | V238A (GTC→GCC) | mreC ← | cell shape determining protein MreC |
| RA | 3,460,262 | A→G | Y149C (TAC→TGC) | gspF → | Type II secretion system protein GspF |
| RA | 3,462,060 | T→C | S29S (AGT→AGC) | gspI → | Type II secretion system protein GspI |
| RA | 3,474,111 | T→C | intergenic (‑30/+67) | rpsG ← / ← rpsL | 30S ribosomal subunit protein S7/30S ribosomal subunit protein S12 |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,594,212 | C→T | E423E (GAG→GAA) | livM ← | branched chain amino acid/phenylalanine ABC transporter membrane subunit LivM |
| RA | 3,625,485 | T→C | S370P (TCA→CCA) | yhhI → | putative transposase |
| RA | 3,633,534 | T→C | pseudogene (925/1607 nt) | yhiL ← | putative uncharacterized protein YhiL |
| RA | 3,670,951 | T→C | Y454H (TAC→CAC) | treF → | cytoplasmic trehalase |
| RA | 3,760,749 | T→C | G167G (GGA→GGG) | selA ← | selenocysteine synthase |
| RA | 3,801,520 | T→C | P160P (CCA→CCG) | waaJ ← | UDP‑glucose:(glucosyl)LPS alpha‑1,2‑glucosyltransferase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,848,073 | A→G | R184R (CGT→CGC) | 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 | 3,880,097 | G→A | S8F (TCC→TTC) | gyrB ← | DNA gyrase subunit B |
| RA | 3,909,551 | T→C | H283R (CAC→CGC) | pstC ← | phosphate ABC transporter membrane subunit PstC |
| RA | 3,931,736 | A→G | T141A (ACC→GCC) | kup → | K(+):H(+) symporter Kup |
| RA | 3,935,558 | G→C | V91L (GTC→CTC) | rbsC → | ribose ABC transporter membrane subunit |
| RA | 3,943,878 | G→A | noncoding (175/2904 nt) | rrlC → | 23S ribosomal RNA |
| RA | 4,023,235 | T→C | V167A (GTC→GCC) | tatC → | twin arginine protein translocation system ‑ TatC protein |
| RA | 4,060,280 | (T)9→8 | intergenic (+50/‑167) | bipA → / → yihL | ribosome‑dependent GTPase, ribosome assembly factor/putative transcriptional regulator YihL |
| RA | 4,130,063 | A→G | T77A (ACG→GCG) | metL → | fused aspartate kinase/homoserine dehydrogenase 2 |
| RA | 4,165,444 | A→G | A602A (GCA→GCG) Q6R (CAG→CGG) |
btuB → murI → |
cobalamin/cobinamide outer membrane transporter glutamate racemase |
| RA | 4,232,933 | C→T | A101T (GCG→ACG) | lysC ← | aspartate kinase III |
| 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 | 4,448,096 | C→T | A68V (GCC→GTC) R50R (AGG→AGA) |
ytfP → yzfA ← |
gamma‑glutamylamine cyclotransferase family protein YtfP putative YjfA |
| RA | 4,449,018 | A→G | L109L (TTA→TTG) | chpB → | endoribonuclease toxin ChpB |
| RA | 4,545,564 | A→G | N157D (AAC→GAC) | fimD → | type I fimbriae usher protein |
| RA | 4,573,528 | A→G | D372G (GAC→GGC) | yjiT → | putative uncharacterized protein YjiT |
| RA | 4,606,094 | (G)8→9 | noncoding (72/87 nt) | leuV ← | tRNA‑Leu |
| RA | 4,637,372 | T→C | V226A (GTT→GCT) | creC → | sensory histidine kinase CreC |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 270638–271294 | 271656–271587 | 294–1019 | 23 [20] | [19] 26 | insI‑1 | IS30 transposase |
| * | * | ÷ | NC_000913 | 729549 | 730412–730147 | 599–864 | 22 [21] | [14] 22 | [rhsC] | [rhsC] |
| * | * | ÷ | NC_000913 | 730547–730565 | 732907–732547 | 1983–2361 | 22 [21] | [21] 22 | rhsC | rhs element protein RhsC |
| * | * | ÷ | NC_000913 | 1269488–1269543 | 1269666–1269593 | 51–179 | 22 [21] | [21] 22 | rdlA/ldrB | putative antisense RNA regulator of LdrA/small toxic polypeptide LdrB |
| * | * | ÷ | NC_000913 | 3423770–3424234 | 3428456–3424653 | 420–4687 | 22 [19] | [20] 22 | [rrfD]–[rrsD] | [rrfD],rrlD,alaU,ileU,[rrsD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 374921 = | NA (NA) | 30 (0.570) | 13/188 | 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 | 374922 = | NA (NA) | 48 (0.670) | 23/258 | 2.1 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377329 = | NA (NA) | intergenic (+18/+206) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 375203 = | NA (NA) | 30 (0.500) | 18/214 | 2.1 | NA | noncoding (17/36 nt) | other | REP31f |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 1207790 = | 64 (0.840) | 32 (0.470) | 29/242 | 1.2 | 39.4% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 42 (0.620) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 64 (0.840) | 24 (0.350) | 21/242 | 2.1 | 32.8% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 42 (0.620) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 64 (0.860) | 49/266 | 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 = | 88 (1.150) | 117 (1.540) | 64/272 | 0.1 | 72.1% | 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) | 93 (1.210) | 59/274 | 0.1 | 98.9% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 1 (0.010) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||