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 | 21,550 | A→G | L48L (TTA→TTG) | ribF → | bifunctional riboflavin kinase/FMN adenylyltransferase |
| RA | 136,457 | (T)8→7 | coding (8/867 nt) | speE ← | spermidine synthase |
| RA | 183,344 | A→G | L294L (TTA→TTG) | cdaR → | DNA‑binding transcriptional activator CdaR |
| RA | 224,989 | A→G | noncoding (1219/1542 nt) | rrsH → | 16S ribosomal RNA |
| RA | 241,304 | A→G | V667A (GTG→GCG) | fadE ← | acyl‑CoA dehydrogenase |
| RA | 244,046 | C→T | A168A (GCC→GCT) | lpcA → | D‑sedoheptulose 7‑phosphate isomerase |
| RA | 253,476 | T→C | pseudogene (10/267 nt) | ykfJ → | conserved protein YkfJ |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 270,495 | (A)5→4 | pseudogene (218/263 nt) | insN → | CP4‑6 prophage; IS911A regulator fragment |
| RA | 319,490 | A→G | V171A (GTT→GCT) | rclA ← | putative pyridine nucleotide‑disulfide oxidoreductase RclA |
| RA | 357,555 | C→T | intergenic (+101/+236) | codA → / ← cynR | cytosine/isoguanine deaminase/DNA‑binding transcriptional dual regulator CynR |
| RA | 359,407 | C→T | A203A (GCC→GCT) | cynT → | carbonic anhydrase 1 |
| RA | 522,573 | G→A | G720R (GGG→AGG) | ybbP → | putative ABC transporter membrane subunit YbbP |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 530,589 | A→G | V213A (GTG→GCG) | selU ← | tRNA 2‑selenouridine synthase |
| RA | 593,034 | A→G | L49L (TTG→CTG) | nfrB ← | bacteriophage N4 receptor, inner membrane subunit |
| RA | 648,427 | A→G | V382A (GTG→GCG) | citF ← | citrate lyase alpha subunit |
| RA | 648,446 | T→C | T376A (ACC→GCC) | citF ← | citrate lyase alpha subunit |
| RA | 790,990 | A→G | Y14H (TAC→CAC) | galT ← | galactose‑1‑phosphate uridylyltransferase |
| RA | 816,962 | T→C | intergenic (‑315/‑82) | ybhK ← / → moaA | putative transferase YbhK/GTP 3',8'‑cyclase |
| 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 | 938,957 | A→G | T322A (ACT→GCT) | rarA → | recombination factor |
| RA | 994,115 | C→T | V240I (GTC→ATC) | ssuC ← | aliphatic sulfonate ABC transporter membrane subunit |
| RA | 1,010,382 | A→G | N140S (AAC→AGC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,126,133 | C→T | T191M (ACG→ATG) | rimJ → | ribosomal‑protein‑S5‑alanine N‑acetyltransferase |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| MC JC | 1,198,490 | (AATGATGA)6→4 | intergenic (‑253/‑190) | ymfE ← / → lit | e14 prophage; uncharacterized protein YmfE/e14 prophage; cell death peptidase Lit |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,360,334 | A→G | V192A (GTT→GCT) | puuA ← | glutamate‑putrescine ligase |
| RA | 1,368,339 | A→G | A87A (GCA→GCG) | pspA → | phage shock protein A |
| RA | 1,376,381 | T→C | R116R (CGT→CGC) | ycjR → | putative ketohexose‑3‑epimerase YcjR |
| RA | 1,512,214 | C→T | G187G (GGC→GGT) | ydcS → | putative ABC transporter periplasmic binding protein/polyhydroxybutyrate synthase |
| RA | 1,514,354 | T→C | V175A (GTG→GCG) | ydcU → | putative ABC transporter membrane subunit YdcU |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,543,373 | A→G | S230P (TCA→CCA) | narU ← | nitrate/nitrite transporter NarU |
| 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 | 1,718,528 | T→C | T359A (ACG→GCG) | anmK ← | anhydro‑N‑acetylmuramic acid kinase |
| RA | 1,748,407 | T→C | V426A (GTC→GCC) | ydhS → | FAD/NAD(P) binding domain‑containing protein YdhS |
| RA | 1,763,967 | T→C | T15A (ACC→GCC) | sufB ← | Fe‑S cluster scaffold complex subunit SufB |
| 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 |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| JC | 2,018,530 | (C)6→9 | coding (145/1128 nt) | fliK → | flagellar hook‑length control protein |
| RA | 2,066,175 | T→C | intergenic (‑411/+130) | cobU ← / ← insH‑6 | cobinamide‑P guanylyltransferase/cobinamide kinase/CP4‑44 prophage; IS5 transposase and trans‑activator |
| 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 | 2,165,953 | T→C | S96P (TCC→CCC) | yegQ → | putative peptidase YegQ |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,244,439 | T→C | V177A (GTC→GCC) | yeiG → | S‑formylglutathione hydrolase/S‑lactoylglutathione hydrolase |
| RA | 2,267,921 | (A)5→4 | coding (93/987 nt) | yeiR → | zinc‑binding GTPase YeiR |
| RA | 2,303,164 | G→A | R112C (CGC→TGC) | napF ← | ferredoxin‑type protein |
| RA | 2,331,932 | T→C | pseudogene (2471/4605 nt) | yfaS ← | putative macroglobulin family protein, N‑terminal fragment |
| RA | 2,364,958 | A→G | L135L (TTA→TTG) | nudI → | pyrimidine deoxynucleotide diphosphatase NudI |
| RA | 2,372,752 | G→A | A66T (GCT→ACT) | arnE → | undecaprenyl‑phosphate‑alpha‑L‑Ara4N flippase ‑ ArnE subunit |
| RA | 2,379,740 | T→C | T302A (ACG→GCG) | menF ← | isochorismate synthase MenF |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,447,002 | T→C | T158A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,460,707 | G→A | I76I (ATC→ATT) | yfcZ ← | DUF406 domain‑containing protein YfcZ |
| RA | 2,473,372 | (T)6→7 | intergenic (‑126/‑232) | yfdO ← / → yfdP | CPS‑53 (KpLE1) prophage; putative defective phage replication protein O/CPS‑53 (KpLE1) prophage; protein YfdP |
| RA | 2,481,904 | (A)8→7 | coding (273/1539 nt) | emrY ← | tripartite efflux pump membrane subunit EmrY |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,599,749 | T→C | G4G (GGA→GGG) | dapA ← | 4‑hydroxy‑tetrahydrodipicolinate synthase |
| RA | 2,682,157 | (C)7→8 | coding (589/3282 nt) | yphG ← | DUF5107 domain‑containing protein YphG |
| RA | 2,701,467 | G→A | P88L (CCA→CTA) | pdxJ ← | pyridoxine 5'‑phosphate synthase |
| RA | 2,732,254 | T→C | K640K (AAA→AAG) | clpB ← | ClpB chaperone |
| RA | 2,734,537 | C→T | G166G (GGG→GGA) | pgeF ← | polyphenol oxidase YfiH |
| RA | 2,799,335 | C→T | P58S (CCA→TCA) | alaE → | L‑alanine exporter |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,871,978 | A→G | R171R (CGT→CGC) | ispD ← | 2‑C‑methyl‑D‑erythritol 4‑phosphate cytidylyltransferase |
| RA | 2,885,766 | G→A | T485I (ACC→ATC) | cas3 ← | CRISPR‑associated endonuclease/helicase Cas3 |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,971,266 | A→G | intergenic (+133/‑5) | ygdQ → / → ygdR | UPF0053 inner membrane protein YgdQ/DUF903 domain‑containing lipoprotein YgdR |
| RA | 2,996,387 | T→C | R297R (AGA→AGG) | insD‑4 ← | IS2 insertion element protein InsB |
| RA | 3,008,069 | T→C | V187A (GTA→GCA) | ygeX → | 2,3‑diaminopropionate ammonia‑lyase |
| RA | 3,052,204 | T→C | E38E (GAA→GAG) | ubiI ← | 2‑octaprenylphenol hydroxylase |
| RA | 3,053,028 | G→A | T164I (ACC→ATC) | ubiH ← | 2‑octaprenyl‑6‑methoxyphenol hydroxylase |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,112,791 | T→C | pseudogene (130/867 nt) | yghF ← | putative type II secretion system C‑type protein |
| RA | 3,159,541 | T→C | M536V (ATG→GTG) | ygiQ ← | radical SAM superfamily protein YgiQ |
| RA | 3,257,809 | (A)5→4 | coding (202/1332 nt) | cyuP ← | putative D/L‑serine transporter |
| RA | 3,331,475 | T→C | T94A (ACG→GCG) | obgE ← | GTPase ObgE |
| RA | 3,353,702 | T→C | T117A (ACC→GCC) | yhcC ← | radical SAM family oxidoreductase YhcC |
| 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 | 3,398,066 | T→C | T105A (ACA→GCA) | yhdE ← | nucleoside triphosphate pyrophosphatase YhdE |
| RA | 3,456,220 | A→T | I215F (ATC→TTC) | gspC → | Type II secretion system protein GspC |
| RA | 3,514,062 | T→C | T110A (ACG→GCG) | gph ← | phosphoglycolate phosphatase |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,569,239 | A→G | G30G (GGT→GGC) | glgC ← | glucose‑1‑phosphate adenylyltransferase |
| RA | 3,765,413 | G→C | A1077A (GCG→GCC) | rhsA → | rhs element protein RhsA |
| 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 | 3,928,600 | A→C | F335C (TTT→TGT) | viaA ← | protein ViaA |
| RA | 3,931,183 | (G)7→8 | intergenic (‑90/‑133) | ravA ← / → kup | regulatory ATPase RavA/K(+):H(+) symporter Kup |
| RA | 3,957,484 | A→G | F113L (TTC→CTC) | ilvY ← | DNA‑binding transcriptional dual regulator IlvY |
| RA | 3,961,438 | T→C | R254R (CGT→CGC) | rep → | ATP‑dependent DNA helicase Rep |
| RA | 4,003,745 | C→A | W145L (TGG→TTG) | rarD ← | putative transporter RarD |
| RA | 4,037,809 | (GT)5→4 | noncoding (291‑292/2905 nt) | rrlA → | 23S ribosomal RNA |
| RA | 4,115,807 | A→G | R472R (CGT→CGC) | glpK ← | glycerol kinase |
| RA | 4,269,117 | T→C | intergenic (‑105/‑297) | yjbS ← / → aphA | uncharacterized protein YjbS/acid phosphatase/phosphotransferase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,299,682 | A→G | V450A (GTG→GCG) | mdtP ← | putative multidrug efflux pump outer membrane channel |
| RA | 4,312,406 | T→G | T196P (ACC→CCC) | alsR ← | DNA‑binding transcriptional repressor AlsR |
| RA | 4,359,713 | A→G | Y107H (TAT→CAT) | cadB ← | lysine:cadaverine antiporter |
| RA | 4,422,159 | A→G | N151S (AAC→AGC) | ulaC → | L‑ascorbate specific PTS enzyme IIA component |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,447,651 | T→C | G1180G (GGT→GGC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,462,837 | T→C | intergenic (‑177/+217) | nrdD ← / ← treC | anaerobic ribonucleoside‑triphosphate reductase/trehalose‑6‑phosphate hydrolase |
| RA | 4,591,161 | A→G | V40A (GTG→GCG) | btsT ← | pyruvate:H(+) symporter |
| JC | 4,606,215 | (G)8→11 | noncoding (72/87 nt) | leuP ← | tRNA‑Leu |
| RA | 4,627,482 | +G | coding (168/1233 nt) | nadR → | DNA‑binding transcriptional repressor/NMN adenylyltransferase NadR |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423491 | 3424525–3424239 | 749–1035 | 15 [14] | [11] 16 | [rrfF]–[rrlD] | [rrfF],thrV,rrfD,[rrlD] |
| * | * | ÷ | NC_000913 | 3619379–3621081 | 3622204–3621086 | 6–2826 | 15 [14] | [13] 15 | rhsB | rhs element protein RhsB |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 76 (1.170) | 17 (0.300) | 15/244 | 2.2 | 22.7% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 49 (0.850) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 1 (0.020) | 46 (0.730) | 37/268 | 0.5 | 99.0% | 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 = | 106 (1.630) | 90 (1.400) | 49/274 | 0.2 | 61.8% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 6 (0.090) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 87 (1.340) | 55/276 | 0.1 | 92.5% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 7 (0.110) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 4542690 | 31 (0.480) | 15 (0.250) | 14/258 | 2.5 | 26.3% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 55 (0.910) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||