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 | 310 | (T)9→8 | intergenic (+55/‑27) | thrL → / → thrA | thr operon leader peptide/fused aspartate kinase/homoserine dehydrogenase 1 |
| RA | 20,601 | G→T | intergenic (‑93/+214) | insA‑1 ← / ← rpsT | IS1 protein InsA/30S ribosomal subunit protein S20 |
| RA | 149,599 | C→T | M1M (ATG→ATA) † | panB ← | 3‑methyl‑2‑oxobutanoate hydroxymethyltransferase |
| RA | 177,992 | A→G | R157R (CGT→CGC) | btuF ← | vitamin B12 ABC transporter periplasmic binding protein |
| RA | 182,227 | T→C | R448R (CGT→CGC) | degP → | periplasmic serine endoprotease DegP |
| RA | 208,270 | A→G | I1049V (ATC→GTC) | dnaE → | DNA polymerase III subunit alpha |
| RA | 215,181 | C→T | R117C (CGC→TGC) | arfB → | peptidyl‑tRNA hydrolase, ribosome rescue factor |
| RA | 223,484 | C→T | intergenic (+76/‑287) | gmhB → / → rrsH | D‑glycero‑beta‑D‑manno‑heptose‑1,7‑bisphosphate 7‑phosphatase/16S ribosomal RNA |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 321,564 | (G)7→6 | intergenic (+483/‑44) | rclR → / → ykgE | DNA‑binding transcriptional activator RclR/putative lactate utilization oxidoreductase YkgE |
| RA | 376,203 | C→T | P249S (CCA→TCA) | mhpT → | 3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| RA | 379,399 | A→G | V58A (GTG→GCG) | frmA ← | S‑(hydroxymethyl)glutathione dehydrogenase |
| JC | 380,022 | (G)10→13 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 383,598 | (A)7→8 | coding (338/1197 nt) | yaiP ← | putative glucosyltransferase |
| RA | 396,598 | A→G | intergenic (‑311/‑41) | ampH ← / → sbmA | peptidoglycan DD‑carboxypeptidase/peptidoglycan DD‑endopeptidase/peptide antibiotic/peptide nucleic acid transporter |
| RA | 506,843 | A→G | G80G (GGT→GGC) | ybaK ← | Cys‑tRNA(Pro) and Cys‑tRNA(Cys) deacylase |
| RA | 513,542 | C→T | R323W (CGG→TGG) | ybaT → | putative transporter YbaT |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 550,467 | (G)5→6 | coding (29/894 nt) | ybcF → | putative carbamate kinase |
| RA | 679,846 | A→G | G113G (GGA→GGG) | ybeU → | DUF1266 domain‑containing protein YbeU |
| RA | 780,262 | A→G | K222R (AAA→AGA) | cpoB → | cell division coordinator CpoB |
| RA | 784,869 | A→G | intergenic (‑46/+68) | zitB ← / ← ybgS | Zn(2(+))/Cd(2(+))/Ni(2(+))/Cu(2(+)) exporter/PF13985 family protein YbgS |
| RA | 815,002 | C→T | R493C (CGT→TGT) | uvrB → | excision nuclease subunit B |
| RA | 863,406 | C→T | E36K (GAA→AAA) | ybiY ← | putative pyruvate formate‑lyase activating enzyme YbiY |
| RA | 868,374 | A→G | R285R (CGA→CGG) | 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 | 922,343 | A→G | intergenic (+50/+23) | macB → / ← cspD | ABC‑type tripartite efflux pump ATP binding/membrane subunit/DNA replication inhibitor |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 996,138 | G→A | R269R (CGC→CGT) | ssuA ← | aliphatic sulfonate ABC transporter periplasmic binding protein |
| RA | 1,004,188 | T→C | L81P (CTG→CCG) | ycbF → | putative fimbrial chaperone YcbF |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,059,436 | (G)6→7 | coding (181/2547 nt) | torA → | trimethylamine N‑oxide reductase 1 |
| RA | 1,070,394 | A→G | S188P (TCC→CCC) | rutE ← | putative malonic semialdehyde reductase |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,212,088 | (C)8→9 | intergenic (‑85/+172) | iraM ← / ← ymgK | anti‑adaptor protein IraM, inhibitor of sigma(S) proteolysis/protein YmgK |
| RA | 1,220,432 | A→G | pseudogene (832/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,226,800 | A→G | L67L (TTA→TTG) | ycgJ → | PF05666 family protein YcgJ |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,311,416 | C→T | P110S (CCA→TCA) | tonB → | Ton complex subunit TonB |
| RA | 1,364,922 | A→G | I231V (ATT→GTT) | puuB → | gamma‑glutamylputrescine oxidase |
| RA | 1,417,275 | A→G | Y38H (TAC→CAC) | recE ← | Rac prophage; exonuclease VIII, ds DNA exonuclease, 5' ‑‑> 3' specific |
| RA | 1,437,231 | (T)9→8 | intergenic (+2/+29) | micC → / ← ydbK | small regulatory RNA MicC/putative pyruvate‑flavodoxin oxidoreductase |
| RA | 1,443,630 | (G)5→6 | coding (580/2640 nt) | ydbH → | PF11739 family protein YdbH |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,609,936 | T→A | I249F (ATT→TTT) | uxaB ← | tagaturonate reductase |
| RA | 1,628,179 | G→T | T221T (ACG→ACT) | ydfG → | 3‑hydroxy acid dehydrogenase |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,669,948 | T→C | L84L (TTG→CTG) | ynfM → | putative transporter YnfM |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,696,443 | C→T | intergenic (‑372/+19) | uidA ← / ← uidR | beta‑glucuronidase/DNA‑binding transcriptional repressor UidR |
| RA | 1,746,411 | G→A | intergenic (‑284/‑24) | ydhQ ← / → valV | adhesin‑like autotransporter YdhQ/tRNA‑Val |
| RA | 1,855,947 | T→C | T9A (ACG→GCG) | ydjG ← | NADH‑dependent methylglyoxal reductase |
| 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 | 1,912,991 | T→C | Y609C (TAC→TGC) | prc ← | tail‑specific protease |
| RA | 1,921,048 | G→A | D276N (GAT→AAT) | rsmF → | 16S rRNA m(5)C1407 methyltransferase |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| MC | 2,067,354 | Δ35,590 bp | between IS5 | yoeA–insH‑7 | 41 genes yoeA, insD‑3, insC‑3, yoeA, yeeP, isrC, flu, yeeR, yeeS, yeeT, cbeA, cbtA, yeeW, yoeF, yeeX, yeeA, sbmC, dacD, sbcB, yeeD, yeeE, plaP, yoeI, yeeY, yeeZ, yoeB, yefM, hisL, hisG, hisD, hisC, hisB, hisH, hisA, hisF, hisI, wzzB, ugd, gnd, wbbL, insH‑7 |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,177,327 | (A)7→6 | intergenic (‑123/+185) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,199,409 | T→C | intergenic (+2111/‑870) | yehF → / → yehI | putative protein YehF/DUF4132 domain‑containing protein YehI |
| RA | 2,201,201 | T→C | V308A (GTC→GCC) | yehI → | DUF4132 domain‑containing protein YehI |
| RA | 2,251,892 | A→G | T65A (ACA→GCA) | yeiI → | putative sugar kinase YeiI |
| RA | 2,258,987 | T→C | T104A (ACC→GCC) | psuK ← | putative pseudouridine kinase |
| RA | 2,262,524 | A→G | G324G (GGT→GGC) | fruB ← | fructose‑specific PTS multiphosphoryl transfer protein FruB |
| RA | 2,276,206 | A→G | T312A (ACC→GCC) | yejE → | putative oligopeptide ABC transporter membrane subunit YejE |
| RA | 2,319,449 | T→C | N143S (AAC→AGC) | rcsC ← | sensory histidine kinase RcsC |
| RA | 2,339,161 | T→C | D87G (GAC→GGC) | gyrA ← | DNA gyrase subunit A |
| RA | 2,373,305 | T→C | E78E (GAA→GAG) | pmrD ← | signal transduction protein PmrD |
| RA | 2,377,547 | A→G | W16R (TGG→CGG) | menH ← | 2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase |
| RA | 2,391,857 | C→T | T395T (ACG→ACA) | nuoM ← | NADH:quinone oxidoreductase subunit M |
| RA | 2,437,716 | C→T | V46I (GTC→ATC) | pdxB ← | erythronate‑4‑phosphate dehydrogenase |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,528,389 | G→A | S596S (AGC→AGT) | ligA ← | DNA ligase |
| RA | 2,599,252 | A→G | V170A (GTA→GCA) | dapA ← | 4‑hydroxy‑tetrahydrodipicolinate synthase |
| RA | 2,750,728 | (T)7→8 | intergenic (‑20/‑103) | grpE ← / → nadK | nucleotide exchange factor GrpE/NAD kinase |
| RA | 2,767,507 | (C)7→6 | intergenic (+152/‑203) | rnlB → / → yfjP | CP4‑57 prophage; antitoxin RnlB/CP4‑57 prophage; putative GTP‑binding protein YfjP |
| RA | 2,778,853 | T→C | T1292A (ACA→GCA) | ypjA ← | adhesin‑like autotransporter YpjA |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,819,417 | G→A | A865A (GCC→GCT) | alaS ← | alanine‑‑tRNA ligase/DNA‑binding transcriptional repressor |
| RA | 2,826,251 | C→T | G140G (GGC→GGT) | srlA → | sorbitol‑specific PTS enzyme IIC2 component |
| RA | 2,847,704 | A→T | L513Q (CTG→CAG) | hycC ← | formate hydrogenlyase subunit HycC |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 3,018,115 | G→A | A686T (GCG→ACG) | ygfK → | putative oxidoreductase, Fe‑S subunit |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,121,914 | T→C | D631G (GAC→GGC) | glcB ← | malate synthase G |
| RA | 3,157,798 | A→G | E50G (GAG→GGG) | yqhG → | DUF3828 domain‑containing protein YqhG |
| RA | 3,177,350 | G→A | N187N (AAC→AAT) | nudF ← | ADP‑sugar pyrophosphatase |
| RA | 3,181,329 | G→A | P303P (CCG→CCA) | ygiC → | putative enzyme with ATPase activity |
| RA | 3,192,444 | (T)7→8 | coding (237/630 nt) | yqiJ → | putative inner membrane protein |
| RA | 3,201,015 | T→C | intergenic (‑50/‑192) | ygiF ← / → ygiM | inorganic triphosphatase/putative signal transduction protein (SH3 domain) |
| RA | 3,307,825 | G→A | G12G (GGC→GGT) | deaD ← | ATP‑dependent RNA helicase DeaD |
| RA | 3,308,664 | T→C | Q87Q (CAA→CAG) | nlpI ← | lipoprotein NlpI |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,367,774 | (C)6→7 | intergenic (+132/‑53) | yhcF → / → yhcG | DUF1120 domain‑containing protein YhcF/DUF1016 domain‑containing protein YhcG |
| RA | 3,368,107 | A→G | Y94C (TAC→TGC) | yhcG → | DUF1016 domain‑containing protein YhcG |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,398,571 | T→C | Q102R (CAG→CGG) | mreD ← | cell shape determining protein MreD |
| RA | 3,419,175 | A→G | pseudogene (134/1025 nt) | yhdW → | putative ABC transporter periplasmic binding protein YhdW |
| RA | 3,434,765 | G→A | L184L (TTG→TTA) | fmt → | 10‑formyltetrahydrofolate:L‑methionyl‑tRNA(fMet) N‑formyltransferase |
| RA | 3,488,175 | G→A | G462D (GGC→GAC) | yhfK → | putative transporter YhfK |
| RA | 3,501,803 | A→T | D179V (GAT→GTT) | frlB → | fructoselysine 6‑phosphate deglycase |
| RA | 3,546,044 | G→A | A141T (GCC→ACC) | nfuA → | iron‑sulfur cluster carrier protein NfuA |
| RA | 3,557,322 | T→C | N253S (AAC→AGC) | rtcB ← | RNA‑splicing ligase |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,622,761 | G→C | R1190R (CGG→CGC) | rhsB → | rhs element protein RhsB |
| RA | 3,623,690 | A→G | T98A (ACC→GCC) | yhhH → | PF15631 family protein YhhH |
| RA | 3,786,954 | A→G | Q39Q (CAA→CAG) | envC → | murein hydrolase activator EnvC |
| 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 | 3,886,465 | T→C | Y464H (TAC→CAC) | yidC → | membrane protein insertase YidC |
| RA | 3,902,316 | (T)8→7 | coding (1386/1413 nt) | bglB ← | 6‑phospho‑beta‑glucosidase B |
| RA | 3,909,781 | A→G | G206G (GGT→GGC) | pstC ← | phosphate ABC transporter membrane subunit PstC |
| RA | 3,982,684 | (C)8→9 | noncoding (79/87 nt) | leuT → | tRNA‑Leu |
| RA | 4,079,416 | A→G | E42E (GAA→GAG) | yiiE → | putative DNA‑binding transcriptional regulator YiiE |
| RA | 4,101,899 | A→G | V70V (GTA→GTG) | kdgT → | 2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,307,237 | C→T | C188Y (TGC→TAC) | alsK ← | D‑allose kinase |
| RA | 4,418,006 | A→G | S150P (TCC→CCC) | ulaR ← | DNA‑binding transcriptional repressor UlaR |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,453,756 | A→G | S58S (TCA→TCG) | yjfF → | galactofuranose ABC transporter putative membrane subunit YjtF |
| RA | 4,520,503 | T→C | intergenic (‑179/+168) | yjhU ← / ← yjhF | KpLE2 phage‑like element; putative DNA‑binding transcriptional regulator YjhU/KpLE2 phage‑like element; putative transporter YjhF |
| RA | 4,606,215 | (G)8→7 | noncoding (72/87 nt) | leuP ← | tRNA‑Leu |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423791–3424234 | 3424530–3424242 | 9–740 | 13 [9] | [11] 12 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 3621202–3622302 | 3622740–3622383 | 82–1539 | 12 [11] | [11] 12 | rhsB | rhs element protein RhsB |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 374921 = | NA (NA) | 25 (0.710) | 10/190 | 1.9 | 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) | 15 (0.400) | 9/202 | 2.3 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377430 = | NA (NA) | intergenic (+119/+105) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 30 (0.850) | 15/190 | 1.1 | 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) | 32 (0.800) | 17/216 | 1.1 | NA | noncoding (17/36 nt) | other | REP31d |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 375203 = | NA (NA) | 22 (0.550) | 13/216 | 1.7 | NA | noncoding (17/36 nt) | other | REP31f |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 1207790 = | 11 (0.210) | 72 (1.590) | 49/244 | 0.0 | 87.4% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 11 (0.240) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 11 (0.210) | 34 (0.750) | 27/244 | 0.6 | 76.6% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 11 (0.240) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 3363001 = | 90 (1.760) | 86 (1.690) | 52/274 | 0.0 | 65.8% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 0 (0.000) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 50 (0.980) | 37/276 | 0.3 | 100% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 0 (0.000) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||