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 | 393 | T→C | R19R (CGT→CGC) | thrA → | fused aspartate kinase/homoserine dehydrogenase 1 |
| RA | 20,724 | G→A | intergenic (‑216/+91) | insA‑1 ← / ← rpsT | IS1 protein InsA/30S ribosomal subunit protein S20 |
| RA | 52,290 | A→G | G47G (GGT→GGC) | rsmA ← | 16S rRNA m(6)2A1518,m(6)2A1519 dimethyltransferase |
| RA | 85,841 | T→C | V71A (GTG→GCG) | ilvI → | acetolactate synthase/acetohydroxybutanoate synthase, catalytic subunit |
| RA | 148,360 | C→T | A146T (GCC→ACC) | panC ← | pantothenate synthetase |
| RA | 222,139 | G→A | S169S (AGC→AGT) | metN ← | L‑methionine/D‑methionine ABC transporter ATP binding subunit |
| RA | 224,700 | C→G | noncoding (930/1542 nt) | rrsH → | 16S ribosomal RNA |
| RA | 282,841 | G→A | P188P (CCG→CCA) | yagE → | CP4‑6 prophage; putative 2‑keto‑3‑deoxygluconate aldolase |
| RA | 286,526 | Δ1 bp | coding (1132/1383 nt) | yagG → | putative D‑xylonate transporter YagG |
| RA | 306,943 | T→C | Y797C (TAC→TGC) | ecpC ← | putative fimbrial usher protein EcpC |
| RA | 308,054 | (C)7→8 | coding (1279/2526 nt) | ecpC ← | putative fimbrial usher protein EcpC |
| RA | 366,805 | C→T | G236S (GGC→AGC) | lacI ← | DNA‑binding transcriptional repressor LacI |
| RA | 368,655 | C→T | S15S (AGC→AGT) | mhpA → | putative 3‑(3‑hydroxyphenyl)propanoate/3‑hydroxycinnamate hydroxylase |
| RA | 380,021 | (G)10→8 | intergenic (‑140/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 410,699 | A→G | T186A (ACC→GCC) | mak → | manno(fructo)kinase |
| RA | 411,095 | C→T | intergenic (+43/+202) | mak → / ← araJ | manno(fructo)kinase/putative transport protein AraJ |
| RA | 443,618 | G→A | C8C (TGC→TGT) P300S (CCT→TCT) |
yajL ← panE ← |
protein/nucleic acid deglycase 3 2‑dehydropantoate 2‑reductase |
| RA | 446,203 | C→T | G155D (GGC→GAC) | yajR ← | putative major facilitator superfamily transport protein YajR |
| RA | 571,081 | T→C | G63G (GGT→GGC) | ybcL → | DLP12 prophage; periplasmic protein YbcL |
| RA | 589,295 | T→C | T554A (ACC→GCC) | nfrA ← | bacteriophage N4 receptor, outer membrane protein |
| RA | 632,017 | (G)7→8 | intergenic (+18/‑165) | cstA → / → ybdD | carbon starvation protein A/conserved protein YbdD |
| RA | 664,090 | G→A | intergenic (‑127/+12) | dacA ← / ← rlpA | D‑alanyl‑D‑alanine carboxypeptidase DacA/rare lipoprotein RlpA |
| RA | 716,988 | A→G | G426G (GGT→GGC) | potE ← | putrescine:H(+) symporter/putrescine:ornithine antiporter PotE |
| RA | 726,108 | C→T | G310D (GGC→GAC) | kdpB ← | K(+) transporting P‑type ATPase subunit KdpB |
| RA | 766,957 | (G)6→5 | coding (974/1977 nt) | mngA → | 2‑O‑alpha‑mannosyl‑D‑glycerate specific PTS enzyme II |
| RA | 796,299 | A→G | L146L (TTA→TTG) | modB → | molybdate ABC transporter membrane subunit |
| RA | 843,613 | C→T | G623D (GGC→GAC) | ybiO ← | moderate conductance mechanosensitive channel |
| RA | 850,986 | (A)6→7 | intergenic (+21/+28) | ompX → / ← opgE | outer membrane protein X/phosphoethanolamine transferase |
| RA | 881,517 | C→T | A264V (GCG→GTG) | dacC → | D‑alanyl‑D‑alanine carboxypeptidase DacC |
| RA | 997,026 | T→C | T163A (ACC→GCC) | ssuE ← | NADPH‑dependent FMN reductase |
| RA | 1,011,394 | A→G | E477E (GAA→GAG) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,075,598 | A→G | G1095G (GGT→GGC) | putA ← | fused DNA‑binding transcriptional repressor/proline dehydrogenase/1‑pyrroline‑5‑carboxylate dehydrogenase PutA |
| RA | 1,151,400 | T→C | V244A (GTC→GCC) | fabG → | 3‑oxoacyl‑[acyl‑carrier‑protein] reductase FabG |
| RA | 1,290,671 | G→A | D144N (GAT→AAT) | rssB → | regulator of RpoS |
| RA | 1,297,869 | T→C | T85A (ACC→GCC) | adhE ← | aldehyde‑alcohol dehydrogenase |
| RA | 1,322,672 | A→G | V92A (GTG→GCG) | trpE ← | anthranilate synthase subunit TrpE |
| RA | 1,418,054 | A→G | V59A (GTC→GCC) | kilR ← | Rac prophage; inhibitor of FtsZ, killing protein |
| RA | 1,480,609 | A→G | E491G (GAG→GGG) | ynbC → | hydrolase/methyltransferase domain‑containing protein YnbC |
| RA | 1,521,295 | G→A | P591S (CCA→TCA) | yncD ← | putative TonB‑dependent outer membrane receptor |
| RA | 1,554,784 | (T)7→8 | coding (886/1698 nt) | maeA ← | malate dehydrogenase, NAD‑requiring |
| RA | 1,594,132 | (C)8→9 | pseudogene (3955/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,674,655 | (C)6→5 | coding (743/1035 nt) | tqsA → | autoinducer 2 exporter |
| RA | 1,679,855 | T→C | V100A (GTC→GCC) | ydgI → | putative arginine:ornithine antiporter |
| RA | 1,692,931 | (T)6→7 | coding (1333/1374 nt) | uidB ← | glucuronide:H(+) symporter |
| RA | 1,750,696 | (C)5→4 | coding (318/669 nt) | ydhX ← | putative 4Fe‑4S ferredoxin‑type protein |
| RA | 1,782,036 | T→C | G214G (GGT→GGC) | ydiS → | putative oxidoreductase with FAD/NAD(P)‑binding domain |
| RA | 1,871,084 | A→G | T234A (ACT→GCT) | cdgI → | putative c‑di‑GMP binding protein CdgI |
| JC JC | 1,873,031 | IS1 (–) +9 bp | coding (991‑999/1491 nt) | dgcJ → | putative diguanylate cyclase DgcJ |
| RA | 1,898,305 | A→G | intergenic (+9/‑122) | sdaA → / → pdeD | L‑serine deaminase I/putative c‑di‑GMP phosphodiesterase PdeD |
| RA | 1,940,196 | T→C | intergenic (‑3/+117) | lpxM ← / ← mepM | myristoyl‑acyl carrier protein‑dependent acyltransferase/peptidoglycan DD‑endopeptidase MepM |
| RA | 1,991,754 | (A)7→6 | intergenic (‑135/+61) | yecA ← / ← leuZ | UPF0149 family protein YecA/tRNA‑Leu |
| RA | 2,059,421 | (A)7→8 | coding (426/1644 nt) | yeeO ← | FMN/FAD exporter |
| RA | 2,182,930 | T→C | Q241R (CAG→CGG) | yegX ← | putative hydrolase |
| RA | 2,232,893 | T→C | F6L (TTC→CTC) | sanA → | DUF218 domain‑containing protein SanA |
| RA | 2,271,477 | G→A | G251D (GGC→GAC) | pdeN → | putative c‑di‑GMP phosphodiesterase PdeN |
| RA | 2,323,945 | T→C | Y167H (TAT→CAT) | atoD → | acetyl‑CoA:acetoacetyl‑CoA transferase subunit alpha |
| RA | 2,370,883 | G→A | C289Y (TGC→TAC) | arnD → | putative 4‑deoxy‑4‑formamido‑L‑arabinose‑phosphoundecaprenol deformylase ArnD |
| RA | 2,446,496 | G→A | I326I (ATC→ATT) | aroC ← | chorismate synthase |
| RA | 2,477,888 | C→T | S14S (AGC→AGT) | dsdX → | D‑serine transporter |
| RA | 2,515,635 | (T)7→6 | intergenic (+192/+8) | insL‑3 → / ← pdeA | putative IS186/IS421 transposase/putative c‑di‑GMP phosphodiesterase PdeA |
| RA | 2,541,092 | T→C | L196L (TTA→TTG) | cysW ← | sulfate/thiosulfate ABC transporter inner membrane subunit CysW |
| RA | 2,544,986 | (C)5→6 | coding (624/858 nt) | murR ← | DNA‑binding transcriptional dual regulator MurR |
| RA | 2,556,529 | T→C | T257A (ACC→GCC) | eutC ← | ethanolamine ammonia‑lyase subunit beta |
| RA | 2,603,973 | C→T | R43C (CGC→TGC) | hyfC → | hydrogenase 4 component C |
| RA | 2,619,813 | C→T | L116L (CTG→CTA) | uraA ← | hypothetical protein |
| RA | 2,682,027 | T→C | D240G (GAC→GGC) | yphG ← | DUF5107 domain‑containing protein YphG |
| RA | 2,737,496 | T→C | intergenic (+1/‑103) | raiA → / → pheL | stationary phase translation inhibitor and ribosome stability factor/phe operon leader peptide |
| RA | 2,758,369 | G→A | Q78* (CAA→TAA) | yfjH ← | CP4‑57 prophage; protein YfjH |
| RA | 2,765,794 | (C)7→6 | intergenic (‑18/‑124) | yfjM ← / → rnlA | CP4‑57 prophage; protein YfjM/CP4‑57 prophage; RNase LS, toxin of the RnlAB toxin‑antitoxin system |
| RA | 2,784,448 | T→C | intergenic (‑19/+81) | ypjB ← / ← ypjC | DUF5508 domain‑containing protein YpjB/DUF5507 domain‑containing protein YpjC |
| RA | 2,827,816 | A→G | Y27C (TAT→TGT) | srlD → | sorbitol‑6‑phosphate 2‑dehydrogenase |
| RA | 2,905,219 | (C)6→7 | coding (200/672 nt) | queE ← | putative 7‑carboxy‑7‑deazaguanine synthase QueE |
| RA | 2,954,256 | T→C | N583S (AAC→AGC) | recB ← | exodeoxyribonuclease V subunit RecB |
| RA | 2,970,379 | G→A | intergenic (+28/‑41) | mutH → / → ygdQ | DNA mismatch repair protein MutH/UPF0053 inner membrane protein YgdQ |
| RA | 2,988,505 | T→C | Y2H (TAC→CAC) | yqeI → | putative transcriptional regulator YqeI |
| RA | 3,171,134 | G→A | R217R (CGG→CGA) | qseC → | sensory histidine kinase QseC |
| RA | 3,177,509 | (C)6→7 | coding (402/630 nt) | nudF ← | ADP‑sugar pyrophosphatase |
| RA | 3,212,282 | T→C | S392S (AGT→AGC) | dnaG → | DNA primase |
| RA | 3,321,233 | C→A | L127F (TTG→TTT) | yhbX ← | putative hydrolase, inner membrane |
| RA | 3,405,422 | T→C | intergenic (+964/‑14) | yhdH → / → accB | acrylyl‑CoA reductase/biotin carboxyl carrier protein |
| RA | 3,432,994 | (C)6→7 | coding (567/1125 nt) | smf ← | protein Smf |
| RA | 3,457,030 | T→C | G218G (GGT→GGC) | gspD → | Type II secretion system protein GspD |
| RA | 3,497,457 | T→C | V152A (GTA→GCA) | nirC → | nitrite transporter NirC |
| RA | 3,584,362 | A→G | intergenic (+53/‑42) | yrhA → / → yrhD | putative uncharacterized protein YrhA/uncharacterized protein YrhD |
| RA | 3,601,037 | C→T | T350T (ACG→ACA) | ftsX ← | cell division protein FtsX |
| RA | 3,603,682 | C→T | E188K (GAA→AAA) | ftsY ← | signal recognition particle receptor |
| RA | 3,734,355 | G→A | P212P (CCG→CCA) | xylH → | xylose ABC transporter membrane subunit |
| RA | 3,756,246 | A→G | I89T (ATT→ACT) | aldB ← | aldehyde dehydrogenase B |
| RA | 3,805,502 | A→G | V150A (GTG→GCG) | waaP ← | lipopolysaccharide core heptose (I) kinase |
| RA | 3,928,483 | C→T | G374D (GGC→GAC) | viaA ← | protein ViaA |
| RA | 3,929,314 | T→C | D97G (GAC→GGC) | viaA ← | protein ViaA |
| RA | 3,930,956 | Δ1 bp | coding (138/1497 nt) | ravA ← | regulatory ATPase RavA |
| RA | 4,011,114 | C→T | F13F (TTC→TTT) | bioP → | biotin transporter |
| RA | 4,015,060 | G→A | D670N (GAC→AAC) | metE → | cobalamin‑independent homocysteine transmethylase |
| RA | 4,047,437 | A→G | T158A (ACC→GCC) | polA → | DNA polymerase I |
| RA | 4,052,006 | A→G | intergenic (+150/‑39) | yihI → / → hemN | Der GTPase‑activating protein YihI/coproporphyrinogen III dehydrogenase |
| RA | 4,061,803 | A→G | E213E (GAA→GAG) | yihM → | putative TIM barrel domain‑containing protein YihM |
| RA | 4,144,401 | T→C | V136A (GTA→GCA) | pflD → | putative formate acetyltransferase 2 |
| RA | 4,204,590 | C→T | A424V (GCC→GTC) | zraR → | DNA‑binding transcriptional activator ZraR |
| RA | 4,218,064 | C→T | S319L (TCG→TTG) | aceA → | isocitrate lyase |
| RA | 4,238,233 | T→A | P200P (CCT→CCA) | yjbH → | YjbH family protein |
| RA | 4,286,180 | A→G | Y398H (TAC→CAC) | acs ← | acetyl‑CoA synthetase (AMP‑forming) |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,380,060 | C→T | G153D (GGT→GAT) | frdB ← | fumarate reductase iron‑sulfur protein |
| RA | 4,419,837 | A→G | intergenic (‑212/‑143) | ulaG ← / → ulaA | L‑ascorbate‑6‑phosphate lactonase/L‑ascorbate specific PTS enzyme IIC component |
| RA | 4,447,243 | C→T | G1044G (GGC→GGT) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,481,603 | A→G | G745G (GGT→GGC) | valS ← | valine‑‑tRNA ligase |
| RA | 4,482,231 | A→G | V536A (GTG→GCG) | valS ← | valine‑‑tRNA ligase |
| RA | 4,595,050 | C→T | A268T (GCT→ACT) | lgoR ← | putative DNA‑binding transcriptional regulator LgoR |
| RA | 4,606,215 | (G)8→9 | noncoding (72/87 nt) | leuP ← | tRNA‑Leu |
| MC JC | 4,612,008 | (GTAATTCGTC)2→1 | intergenic (+7/‑111) | osmY → / → ytjA | periplasmic chaperone OsmY/DUF1328 domain‑containing protein YtjA |
| RA | 4,622,927 | T→C | F387L (TTT→CTT) | yjjJ → | toxin YjjJ |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 361198 | 361912 | 715 | 225 [223] | [222] 224 | lacA | lacA |
| * | * | ÷ | NC_000913 | 2066221–2066464 | 2067226–2066466 | 3–1006 | 227 [220] | [208] 226 | [insH‑6] | [insH‑6] |
| * | * | ÷ | NC_000913 | 2856995 | 2857095 | 101 | 224 [220] | [0] 400 | [mutS] | [mutS] |
| * | * | ÷ | NC_000913 | 3423675–3424234 | 3424616–3424238 | 5–942 | 226 [219] | [222] 228 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 70046 = | 394 (1.090) | 387 (1.100) | 173/188 | 0.0 | 67.0% | coding (3/1701 nt) | araB | ribulokinase |
| ? | NC_000913 | 2857096 = | 0 (0.000) | coding (4/2562 nt) | mutS | DNA mismatch repair protein MutS | |||||