mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| JC JC | 57,276 | IS2 (+) +5 bp | intergenic (‑167/‑84) | lptD ← / → djlA | lipopolysaccharide assembly protein LptD/co‑chaperone protein DjlA |
| RA | 71,134 | G→A | G250S (GGT→AGT) | araC → | DNA‑binding transcriptional dual regulator AraC |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 490,657 | C→T | E52E (GAG→GAA) | priC ← | primosomal replication protein N'' |
| RA | 499,839 | C→T | T45T (ACG→ACA) | aes ← | acetylesterase |
| RA | 502,658 | C→T | G194D (GGC→GAC) | ybaL ← | putative transporter YbaL |
| RA | 507,310 | C→T | G257G (GGG→GGA) | ybaP ← | TraB family protein YbaP |
| RA | 557,635 | A→T | L36Q (CTG→CAG) | folD ← | bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase |
| JC JC | 568,449 | IS2 (–) +5 bp | coding (135‑139/333 nt) | emrE → | multidrug/betaine/choline efflux transporter EmrE |
| RA | 627,802 | G→A | D37N (GAT→AAT) | entB → | enterobactin synthase component B |
| RA | 630,722 | G→A | A277T (GCC→ACC) | cstA → | pyruvate transporter CstA |
| RA | 631,633 | G→A | W580* (TGG→TGA) | cstA → | pyruvate transporter CstA |
| RA | 637,579 | G→A | L14F (CTT→TTT) | ybdO ← | putative LysR family DNA‑binding transcriptional regulator YbdO |
| RA | 642,276 | G→A | M63I (ATG→ATA) | ybdR → | putative Zn(2(+))‑dependent alcohol dehydrogenase YbdR |
| RA | 642,902 | G→A | S272N (AGC→AAC) | ybdR → | putative Zn(2(+))‑dependent alcohol dehydrogenase YbdR |
| RA | 651,068 | G→A | P263P (CCC→CCT) | citC ← | citrate lyase synthetase |
| RA | 660,875 | G→A | I168I (ATC→ATT) | ybeF ← | putative DNA‑binding transcriptional regulator YbeF |
| RA | 677,274 | G→A | A188A (GCG→GCA) | ybeR → | DUF1266 domain‑containing protein YbeR |
| RA | 726,271 | C→T | V256M (GTG→ATG) | kdpB ← | K(+) transporting P‑type ATPase subunit KdpB |
| RA | 732,944 | C→T | S1121L (TCG→TTG) | rhsC → | rhs element protein RhsC |
| RA | 734,412 | C→T | intergenic (+310/‑1238) | ybfB → / → ybfC | uncharacterized protein YbfB/uncharacterized protein YbfC |
| RA | 734,537 | C→T | intergenic (+435/‑1113) | ybfB → / → ybfC | uncharacterized protein YbfB/uncharacterized protein YbfC |
| RA | 740,000 | G→A | G165E (GGG→GAG) | phr → | deoxyribodipyrimidine photolyase |
| RA | 741,299 | G→A | L420L (CTG→TTG) | dtpD ← | dipeptide:H(+) symporter DtpD |
| RA | 761,705 | G→A | E62K (GAA→AAA) | sucB → | dihydrolipoyltranssuccinylase |
| RA | 771,261 | G→A | intergenic (+650/‑197) | mngB → / → cydA | alpha‑mannosidase/cytochrome bd‑I subunit 1 |
| RA | 778,995 | G→A | G419E (GGA→GAA) | tolB → | Tol‑Pal system periplasmic protein TolB |
| RA | 783,682 | G→A | A173T (GCA→ACA) | pnuC → | nicotinamide riboside transporter |
| RA | 815,427 | G→A | Q634Q (CAG→CAA) | uvrB → | UvrABC excision nuclease subunit B |
| RA | 827,118 | G→A | Y45Y (TAC→TAT) | ybhS ← | ABC exporter membrane subunit YbhS |
| RA | 842,562 | C→T | C77C (TGC→TGT) | rlmF → | 23S rRNA m(6)A1618 methyltransferase |
| RA | 851,900 | C→T | G233D (GGT→GAT) | opgE ← | phosphoethanolamine transferase OpgE |
| RA | 858,241 | C→T | G274E (GGG→GAG) | ybiU ← | DUF1479 domain‑containing protein YbiU |
| RA | 864,973 | C→T | A53T (GCC→ACC) | moeB ← | molybdopterin‑synthase adenylyltransferase |
| RA | 871,126 | C→T | Q54* (CAG→TAG) | gsiC → | glutathione ABC transporter membrane subunit GsiC |
| RA | 950,079 | C→T | Q138* (CAG→TAG) | ycaK → | putative oxidoreductase YcaK |
| RA | 969,089 | C→T | P242S (CCG→TCG) | lpxK → | tetraacyldisaccharide 4'‑kinase |
| RA | 976,108 | C→T | R163C (CGT→TGT) | mukE → | chromosome partitioning protein MukE |
| RA | 987,152 | G→T | intergenic (‑170/+433) | ompF ← / ← asnS | outer membrane porin F/asparagine‑‑tRNA ligase |
| RA | 987,592 | C→T | S465N (AGC→AAC) | asnS ← | asparagine‑‑tRNA ligase |
| RA | 1,008,732 | C→T | P297S (CCG→TCG) | rlmL → | fused 23S rRNA m(2)G2445 methyltransferase and 23S rRNA m(7)G2069 methyltransferase |
| RA | 1,023,482 | C→T | E134E (GAG→GAA) | yccS ← | putative transporter YccS |
| RA | 1,032,730 | C→T | P198S (CCG→TCG) | hyaA → | hydrogenase 1 small subunit |
| RA | 1,082,747 | G→A | A169T (GCG→ACG) | efeO → | ferrous iron transport system protein EfeO |
| JC JC | 1,105,376 | IS2 (–) +5 bp | intergenic (+83/‑34) | csgC → / → ymdA | curlin chaperone/uncharacterized protein YmdA |
| RA | 1,196,220 | C→T | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,232 | C→T | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,245 | T→C | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,247 | A→G | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,227,090 | A→G | V128A (GTC→GCC) | pliG ← | inhibitor of g‑type lysozyme |
| RA | 1,290,881 | C→T | L214F (CTT→TTT) | rssB → | regulator of RpoS |
| MC JC | 1,294,035 | Δ141 bp | [tdk] | [tdk] | |
| MC JC | 1,303,073 | Δ12 bp | coding (175‑186/921 nt) | oppB → | murein tripeptide ABC transporter/oligopeptide ABC transporter inner membrane subunit OppB |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,353,758 | T→A | D254V (GAT→GTT) | sapC ← | putrescine ABC exporter membrane protein SapC |
| RA | 1,494,388 | Δ1 bp | coding (684/924 nt) | ydcI ← | DNA‑binding transcriptional dual regulator YdcI |
| RA | 1,517,508 | G→T | V40V (GTG→GTT) | ortT → | orphan toxin OrtT |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,667,887 | Δ1 bp | coding (678/1221 nt) | mlc ← | DNA‑binding transcriptional repressor Mlc |
| RA | 1,744,751 | Δ1 bp | coding (1295/1374 nt) | mdtK → | multidrug efflux pump MdtK |
| JC JC | 1,792,772 | IS2 (–) +5 bp | intergenic (‑41/+33) | nlpC ← / ← btuD | NlpC/P60 family lipoprotein NlpC/vitamin B12 ABC transporter ATP binding subunit |
| RA | 1,978,243 | G→T | intergenic (‑46/+275) | flhD ← / ← insB5 | DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB |
| RA | 2,003,264 | C→T | E115K (GAA→AAA) | fliC ← | flagellar filament structural protein |
| RA | 2,032,423 | G→A | V219V (GTC→GTT) | yedJ ← | putative HD superfamily phosphohydrolase YedJ |
| RA | 2,132,762 | C→T | M212I (ATG→ATA) | wcaA ← | UDP‑glucuronate:2‑O‑Ac‑beta‑D‑Gal‑(1‑>3)‑alpha‑ L‑Fuc‑(1‑>4)‑2/3‑O‑Ac‑alpha‑L‑Fuc‑(1‑>3)‑beta‑D‑Glc‑PP‑Und beta‑(1,3)‑glucuronosyltransferase |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| RA | 2,188,042 | C→T | G125R (GGG→AGG) | yehA ← | putative fimbrial adhesin YehA |
| RA | 2,206,654 | C→T | A320A (GCC→GCT) | yehM → | uncharacterized protein YehM |
| RA | 2,238,848 | C→T | G148S (GGC→AGC) | mglA ← | D‑galactose/methyl‑galactoside ABC transporter ATP binding subunit |
| RA | 2,242,121 | A→G | S283P (TCG→CCG) | yeiB ← | DUF418 domain‑containing protein YeiB |
| RA | 2,253,098 | C→T | A350T (GCT→ACT) | nupX ← | putative nucleoside transporter |
| RA | 2,259,260 | C→T | A13T (GCG→ACG) | psuK ← | putative pseudouridine kinase |
| RA | 2,261,603 | C→T | D255N (GAT→AAT) | fruK ← | 1‑phosphofructokinase |
| JC JC | 2,269,876 | IS5 (+) +4 bp | intergenic (+309/‑100) | lpxT → / → mepS | lipid A‑core phosphotransferase/peptidoglycan endopeptidase/peptidoglycan L,D‑carboxypeptidase |
| JC JC | 2,319,850 | IS2 (+) +5 bp | coding (23‑27/2850 nt) | rcsC ← | histidine kinase RcsC |
| RA | 2,397,444 | G→A | Q908* (CAA→TAA) | nuoG ← | NADH:quinone oxidoreductase subunit G |
| JC JC | 2,406,780 | IS1 (–) +8 bp | intergenic (‑139/‑774) | lrhA ← / → alaA | DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA |
| MC JC | 2,558,699 | Δ6,790 bp | intZ–[eutA] | intZ, yffL, yffM, yffN, yffO, yffP, yffQ, yffR, yffS, [eutA] | |
| JC JC | 2,666,074 | IS1 (+) +9 bp | coding (640‑648/1281 nt) | csiE → | stationary phase‑inducible protein CsiE |
| RA | 3,198,612 | G→A | L344L (CTG→TTG) | glnE ← | fused glutamine synthetase deadenylase/glutamine synthetase adenylyltransferase |
| RA | 3,268,970 | A→G | T186A (ACA→GCA) | yhaC → | uncharacterized protein YhaC |
| RA | 3,332,719 | C→T | G6D (GGC→GAC) | yhbE ← | putative transporter YhbE |
| RA | 3,412,158 | C→T | P169L (CCT→CTT) | yhdJ → | DNA adenine methyltransferase |
| RA | 3,486,205 | C→A | T29K (ACG→AAG) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,637,714 | T→C | F25L (TTC→CTC) | pitA → | metal phosphate:H(+) symporter PitA |
| RA | 3,638,857 | G→A | A406T (GCA→ACA) | pitA → | metal phosphate:H(+) symporter PitA |
| RA | 3,643,200 | G→A | R661R (CGC→CGT) | prlC ← | oligopeptidase A |
| RA | 3,659,888 | C→T | F219F (TTC→TTT) | mdtE → | multidrug efflux pump membrane fusion protein MdtE |
| RA | 3,670,835 | C→T | S415F (TCC→TTC) | treF → | cytoplasmic trehalase |
| RA | 3,674,009 | C→T | A216A (GCC→GCT) | yhjD → | putative transporter YhjD |
| RA | 3,678,147 | G→A | G68G (GGC→GGT) | yhjG ← | AsmA family protein YhjG |
| MC JC | 3,682,261 | Δ34 bp | coding (1154‑1187/1287 nt) | dctA ← | C4 dicarboxylate/orotate:H(+) symporter |
| RA | 3,685,723 | G→A | L1151L (CTG→TTG) | bcsC ← | cellulose synthase outer membrane channel |
| RA | 3,694,888 | G→A | H117Y (CAT→TAT) | bcsA ← | cellulose synthase catalytic subunit |
| RA | 3,698,513 | G→A | G100G (GGG→GGA) | bcsG → | cellulose phosphoethanolamine transferase |
| RA | 3,712,552 | G→A | T128I (ACT→ATT) | yhjY ← | putative outer membrane protein YhjY |
| RA | 3,714,550 | G→A | C615C (TGC→TGT) | bisC ← | biotin sulfoxide reductase |
| RA | 3,722,122 | G→A | intergenic (+73/+206) | insK → / ← glyS | IS150 family conserved protein InsB/glycine‑‑tRNA ligase subunit beta |
| RA | 3,723,019 | G→A | T460I (ACC→ATC) | glyS ← | glycine‑‑tRNA ligase subunit beta |
| RA | 3,723,853 | G→A | S182F (TCC→TTC) | glyS ← | glycine‑‑tRNA ligase subunit beta |
| RA | 3,727,551 | G→A | I66I (ATC→ATT) | yiaB ← | PF05360 family inner membrane protein YiaB |
| RA | 3,728,083 | C→T | R430K (AGG→AAG) | xylB ← | xylulokinase |
| JC JC | 3,737,137 | IS2 (+) +5 bp | coding (37‑41/825 nt) | bax ← | putative glycoside hydrolase Bax |
| RA | 3,742,379 | C→T | A52T (GCT→ACT) | plaR ← | DNA‑binding transcriptional repressor PlaR |
| RA | 3,745,511 | C→T | T236T (ACC→ACT) | yiaN → | 2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ membrane subunit |
| RA | 3,747,734 | C→T | I217I (ATC→ATT) | lyxK → | L‑xylulose kinase |
| RA | 3,749,315 | C→T | S28S (AGC→AGT) | sgbU → | putative L‑xylulose 5‑phosphate 3‑epimerase |
| RA | 3,751,676 | C→T | G65S (GGT→AGT) | yiaT ← | outer membrane protein YiaT |
| RA | 4,037,994 | G→A | noncoding (476/2905 nt) | rrlA → | 23S ribosomal RNA |
| RA | 4,065,373 | G→A | L132L (CTG→TTG) | yihO ← | putative sulfoquinovose transporter |
| RA | 4,073,830 | G→A | R31K (AGA→AAA) | yihV → | 6‑deoxy‑6‑sulfofructose kinase |
| RA | 4,073,894 | G→A | G52G (GGG→GGA) | yihV → | 6‑deoxy‑6‑sulfofructose kinase |
| RA | 4,093,306 | G→A | L45F (CTC→TTC) | rhaM ← | L‑rhamnose mutarotase |
| RA | 4,094,504 | G→A | intergenic (‑232/+219) | rhaD ← / ← rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| RA | 4,097,140 | G→A | R103R (CGC→CGT) | rhaB ← | rhamnulokinase |
| RA | 4,097,365 | G→A | R28R (CGC→CGT) | rhaB ← | rhamnulokinase |
| RA | 4,104,526 | G→A | S150S (AGC→AGT) | cpxA ← | sensor histidine kinase CpxA |
| JC JC | 4,123,923 | IS2 (–) +5 bp | coding (530‑534/1026 nt) | cytR ← | DNA‑binding transcriptional repressor CytR |
| JC JC | 4,135,180 | IS2 (–) +5 bp | coding (1346‑1350/2181 nt) | katG → | catalase/hydroperoxidase HPI |
| RA | 4,146,389 | (T)6→7 | coding (132/879 nt) | pflC → | putative pyruvate formate‑lyase 2 activating enzyme PflC |
| RA | 4,184,322 | G→A | E1026E (GAG→GAA) | rpoB → | RNA polymerase subunit beta |
| RA | 4,202,058 | G→A | D45N (GAC→AAC) | zraS → | sensor histidine kinase ZraS |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,378,974 | C→T | intergenic (‑30/+33) | ampC ← / ← frdD | beta‑lactamase/fumarate reductase membrane protein FrdD |
| JC JC | 4,536,236 | IS5 (+) +4 bp | intergenic (‑2183/‑358) | topAI ← / → ythB | toxin of the TopAI‑YjhQ toxin‑antitoxin system, TopA inhibitor/protein YthB |
| RA | 4,542,683 | Δ1 bp | intergenic (+50/‑432) | fimE → / → fimA | regulator for fimA/type 1 fimbriae major subunit |
| RA | 4,572,571 | T→C | V53A (GTC→GCC) | yjiT → | putative uncharacterized protein YjiT |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196266 | 1211460 | 15195 | 41 [33] | [33] 37 | [icd]–mcrA | [icd],C0293,ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,ymfN,ymfR,beeE,ymfQ,ycfK,tfaP,tfaE,pinE,mcrA |
| * | * | ÷ | NC_000913 | 1978495 | 1979270–1978504 | 10–776 | 101 [0] | [1] 132 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 3423806–3424234 | 3424485–3424238 | 5–680 | 36 [34] | [34] 35 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 3619460–3621083 | 3622134–3621090 | 8–2675 | 35 [33] | [33] 35 | rhsB | rhs element protein RhsB |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 381260 = | NA (NA) | 78 (0.760) | 59/598 | 0.5 | NA | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382183 | NA (NA) | noncoding (924/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 119 (1.170) | 71/590 | 0.2 | 100% | intergenic (+253/‑69) | ychE/insH21 | MarC family putative inner membrane protein YchE/IS5 family transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 100 (0.970) | 74/598 | 0.2 | 100% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1978494 | 0 (0.000) | intergenic (‑297/+24) | flhD/insB5 | DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB | |||||
| * | ? | NC_000913 | 1979271 = | 1 (0.010) | 131 (1.270) | 92/598 | 0.0 | 99.2% | intergenic (‑56/‑482) | insA5/uspC | IS1 family protein InsA/universal stress protein C |
| ? | NC_000913 | = 2102947 | NA (NA) | pseudogene (443/446 nt) | wbbL | interrupted rhamnosyltransferase WbbL | |||||