mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.0b
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 256,243 | A→G | 6.4% | T49A (ACG→GCG) | proB → | gamma‑glutamate kinase |
| RA | 326,966 | T→C | 4.9% | V598A (GTC→GCC) | betT → | choline transporter of high affinity |
| RA | 416,397 | T→A | 7.7% | intergenic (+31/‑45) | brnQ → / → proY | branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val/proline‑specific permease |
| RA | 416,398 | G→T | 7.7% | intergenic (+32/‑44) | brnQ → / → proY | branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val/proline‑specific permease |
| RA | 416,401 | A→C | 7.7% | intergenic (+35/‑41) | brnQ → / → proY | branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val/proline‑specific permease |
| RA | 416,402 | T→A | 7.8% | intergenic (+36/‑40) | brnQ → / → proY | branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val/proline‑specific permease |
| RA | 454,949 | G→T | 26.8% | S202S (TCG→TCT) | lon → | DNA‑binding ATP‑dependent protease La |
| RA | 463,920 | Δ1 bp | 30.4% | coding (82/459 nt) | ybaO → | putative DNA‑binding transcriptional regulator |
| RA | 468,056 | G→T | 17.7% | M1M (ATG→ATT) † | glnK → | nitrogen assimilation regulatory protein for GlnL, GlnE, and AmtB |
| RA | 468,288 | A→T | 35.6% | K79* (AAG→TAG) | glnK → | nitrogen assimilation regulatory protein for GlnL, GlnE, and AmtB |
| RA | 753,013 | G→T | 56.0% | E551* (GAA→TAA) | sdhA → | succinate dehydrogenase, flavoprotein subunit |
| RA | 766,135 | G→T | 6.9% | intergenic (+68/‑779) | mngB → / → cydA | alpha‑mannosidase/cytochrome d terminal oxidase, subunit I |
| RA | 766,138 | A→C | 7.2% | intergenic (+71/‑776) | mngB → / → cydA | alpha‑mannosidase/cytochrome d terminal oxidase, subunit I |
| RA | 1,067,611 | G→T | 5.7% | P2Q (CCA→CAA) | rutC ← | putative aminoacrylate deaminase, reactive intermediate detoxification; weak enamine/imine deaminase activity |
| RA | 1,191,676 | C→T | 31.1% | H366H (CAC→CAT) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,688 | C→T | 29.0% | T370T (ACC→ACT) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,701 | T→C | 24.0% | L375L (TTA→CTA) ‡ | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,703 | A→G | 26.5% | L375L (TTA→TTG) ‡ | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,733 | C→T | 18.8% | N385N (AAC→AAT) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,736 | G→C | 18.7% | A386A (GCG→GCC) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,739 | A→G | 19.7% | K387K (AAA→AAG) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,748 | C→T | 17.6% | T390T (ACC→ACT) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,760 | G→A | 13.4% | E394E (GAG→GAA) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,460,602 | T→C | 9.9% | pseudogene (954/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 2,298,277 | T→C | 13.2% | intergenic (+405/+310) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| JC JC | 2,400,257 | IS5 (+) +4 bp | 53.7% | intergenic (‑137/‑780) | lrhA ← / → alaA | transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2 |
| RA | 2,419,720 | T→C | 11.2% | D183G (GAT→GGT) | hisJ ← | histidine/lysine/arginine/ornithine transporter subunit |
| RA | 2,420,353 | A→T | 58.7% | intergenic (‑86/+135) | hisJ ← / ← argT | histidine/lysine/arginine/ornithine transporter subunit/lysine/arginine/ornithine transporter subunit |
| RA | 2,519,265:1 | +A | 3.9% | intergenic (+15/+24) | yfeN → / ← yfeR | putative outer membrane protein/transcriptional regulator of yefH |
| RA | 2,519,268 | Δ1 bp | 3.8% | intergenic (+18/+21) | yfeN → / ← yfeR | putative outer membrane protein/transcriptional regulator of yefH |
| RA | 2,524,024 | C→T | 3.8% | R190H (CGC→CAC) | zipA ← | FtsZ stabilizer |
| RA | 2,621,636 | A→G | 5.0% | L221P (CTG→CCG) | yfgF ← | cyclic‑di‑GMP phosphodiesterase, anaerobic |
| RA | 2,718,678 | C→G | 30.7% | G143A (GGC→GCC) | kgtP ← | alpha‑ketoglutarate transporter |
| RA | 2,718,882 | A→G | 10.4% | M75T (ATG→ACG) | kgtP ← | alpha‑ketoglutarate transporter |
| RA | 2,719,426 | T→C | 43.6% | intergenic (‑321/+2) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,860,628 | T→A | 38.8% | I95F (ATC→TTC) | rpoS ← | RNA polymerase, sigma S (sigma 38) factor |
| RA | 2,861,917 | G→A | 40.6% | Q66* (CAG→TAG) | nlpD ← | activator of AmiC murein hydrolase activity, lipoprotein |
| RA | 2,870,339 | G→A | 38.4% | G134S (GGC→AGC) | iap → | aminopeptidase in alkaline phosphatase isozyme conversion |
| RA | 2,964,505 | T→C | 6.6% | intergenic (+13/‑125) | ygdQ → / → ygdR | UPF0053 family inner membrane protein/DUF903 family verified lipoprotein |
| RA | 2,964,510 | T→C | 5.1% | intergenic (+18/‑120) | ygdQ → / → ygdR | UPF0053 family inner membrane protein/DUF903 family verified lipoprotein |
| RA | 2,964,513 | G→A | 6.2% | intergenic (+21/‑117) | ygdQ → / → ygdR | UPF0053 family inner membrane protein/DUF903 family verified lipoprotein |
| RA | 2,964,518 | G→A | 4.9% | intergenic (+26/‑112) | ygdQ → / → ygdR | UPF0053 family inner membrane protein/DUF903 family verified lipoprotein |
| RA | 3,019,631 | G→T | 41.1% | M169I (ATG→ATT) | guaD → | guanine deaminase |
| RA | 3,029,079 | C→T | 39.9% | A188T (GCT→ACT) | prfB ← | peptide chain release factor RF‑2 |
| RA | 3,173,856 | Δ1 bp | 5.3% | coding (77/1161 nt) | ygiC → | ATP‑Grasp family ATPase |
| RA | 3,173,864 | G→T | 4.8% | E29* (GAG→TAG) ‡ | ygiC → | ATP‑Grasp family ATPase |
| RA | 3,173,865 | A→C | 6.0% | E29A (GAG→GCG) ‡ | ygiC → | ATP‑Grasp family ATPase |
| JC JC | 3,178,254 | IS5 (+) +4 bp | 43.7% | coding (56‑59/291 nt) | yqiC → | BMFP family putative fusogenic protein |
| RA | 3,204,161 | G→A | 34.4% | E8K (GAA→AAA) | rpsU → | 30S ribosomal subunit protein S21 |
| RA | 3,241,196 | Δ1 bp | 6.1% | coding (65/663 nt) | yqjA → | general envelope maintenance protein; DedA family inner membrane protein |
| RA | 3,241,203:1 | +G | 6.1% | coding (72/663 nt) | yqjA → | general envelope maintenance protein; DedA family inner membrane protein |
| RA | 3,385,528 | T→C | 5.0% | intergenic (‑141/+289) | tldD ← / ← yhdP | putative peptidase/DUF3971‑AsmA2 domains protein |
| RA | 3,960,102 | G→T | 31.4% | R109L (CGC→CTC) | rho → | transcription termination factor |
| RA | 4,245,568 | T→C | 6.0% | N276S (AAC→AGC) | plsB ← | glycerol‑3‑phosphate O‑acyltransferase |
| RA | 4,390,205 | G→T | 52.5% | G34V (GGG→GTG) | hfq → | global sRNA chaperone; HF‑I, host factor for RNA phage Q beta replication |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 15387 = | NA (NA) | 6 (0.090) | 6/262 | NT | 12.5% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | CP009273 | = 454251 | 42 (0.620) | intergenic (+95/‑93) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La | |||||
| * | ? | CP009273 | = 270406 | NA (NA) | 3 (0.040) | 3/262 | NT | NA | noncoding (201/335 nt) | IS911 | repeat region |
| ? | CP009273 | = 270438 | NA (NA) | noncoding (233/335 nt) | IS911 | repeat region | |||||
| * | ? | CP009273 | 301106 = | 78 (1.120) | 3 (0.040) | 3/260 | NT | 4.0% | coding (1423/1644 nt) | ecpD | polymerized tip adhesin of ECP fibers |
| ? | CP009273 | 301143 = | 68 (1.010) | coding (1386/1644 nt) | ecpD | polymerized tip adhesin of ECP fibers | |||||
| * | ? | CP009273 | 345316 = | NA (NA) | 4 (0.060) | 3/256 | NT | NA | noncoding (1/365 nt) | REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences | REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences |
| ? | CP009273 | 345348 = | NA (NA) | noncoding (33/365 nt) | REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences | REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences | |||||
| * | ? | CP009273 | 360104 = | NA (NA) | 128 (1.830) | 89/270 | NT | NA | intergenic (‑38/+557) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | = 360286 | NA (NA) | intergenic (‑220/+375) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor | |||||
| * | ? | CP009273 | 416386 = | 64 (0.910) | 3 (0.050) | 5/248 | NT | 4.8% | intergenic (+20/‑56) | brnQ/proY | branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val/proline‑specific permease |
| ? | CP009273 | 416414 = | 59 (0.920) | intergenic (+48/‑28) | brnQ/proY | branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val/proline‑specific permease | |||||
| * | ? | CP009273 | 454243 = | 42 (0.600) | 11 (0.160) | 9/264 | NT | 21.1% | intergenic (+87/‑101) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| ? | CP009273 | = 604803 | NA (NA) | intergenic (+170/+112) | insL1/entD | IS186 transposase/phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex | |||||
| * | ? | CP009273 | 617413 = | 70 (1.000) | 4 (0.060) | 4/258 | NT | 6.4% | coding (233/1005 nt) | fepD | iron‑enterobactin transporter subunit |
| ? | CP009273 | 617513 = | 51 (0.760) | coding (133/1005 nt) | fepD | iron‑enterobactin transporter subunit | |||||
| * | ? | CP009273 | 1203246 = | 26 (0.370) | 16 (0.260) | 14/238 | NT | 40.0% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 25 (0.410) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 26 (0.370) | 19 (0.310) | 18/238 | NT | 44.2% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 25 (0.410) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1391495 | NA (NA) | 33 (0.470) | 27/270 | NT | 49.3% | intergenic (+146/‑127) | insH1/ynaJ | IS5 transposase and trans‑activator/DUF2534 family putative inner membrane protein |
| ? | CP009273 | = 1972751 | 34 (0.490) | intergenic (‑297/‑483) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein | |||||
| * | ? | CP009273 | = 1515197 | 33 (0.470) | 2 (0.030) | 3/254 | NT | 5.9% | intergenic (+13/+23) | mcbR/yncD | colanic acid and biofilm gene transcriptional regulator, MqsR‑controlled/putative iron outer membrane transporter |
| ? | CP009273 | = 1515203 | 33 (0.500) | intergenic (+19/+17) | mcbR/yncD | colanic acid and biofilm gene transcriptional regulator, MqsR‑controlled/putative iron outer membrane transporter | |||||
| * | ? | CP009273 | 1810442 = | NA (NA) | 3 (0.050) | 3/256 | NT | NA | noncoding (1/189 nt) | RIP129 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site | RIP129 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site |
| ? | CP009273 | 1810472 = | NA (NA) | noncoding (31/189 nt) | RIP129 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site | RIP129 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site | |||||
| * | ? | CP009273 | = 1874094 | 41 (0.590) | 4 (0.060) | 3/264 | NT | 9.1% | coding (112/360 nt) | yeaR | DUF1971 family protein, nitrate‑inducible |
| ? | CP009273 | = 2509092 | NA (NA) | intergenic (+170/+30) | insL1/yfeA | IS186 transposase/putative diguanylate cyclase | |||||
| * | ? | CP009273 | 1972748 = | 35 (0.500) | 46 (0.660) | 34/268 | NT | 56.8% | intergenic (‑294/‑486) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein |
| ? | CP009273 | = 2283592 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | CP009273 | 2269338 = | 20 (0.290) | 42 (0.600) | 32/270 | NT | 67.7% | coding (587/1026 nt) | yejE | microcin C transporter YejABEF, permease subunit; ABC family |
| ? | CP009273 | = 3577555 | NA (NA) | intergenic (+15/‑1) | insB1/yrhA | IS1 transposase B/pseudogene, interrupted by IS1E | |||||
| * | ? | CP009273 | = 2269346 | 24 (0.340) | 39 (0.560) | 30/270 | NT | 61.9% | coding (595/1026 nt) | yejE | microcin C transporter YejABEF, permease subunit; ABC family |
| ? | CP009273 | 3576788 = | NA (NA) | intergenic (+10/‑55) | yrhA/insA | pseudogene, interrupted by IS1E/IS1 repressor TnpA | |||||
| * | ? | CP009273 | 2419417 = | 96 (1.370) | 5 (0.070) | 3/258 | NT | 5.0% | intergenic (‑22/+68) | hisQ/hisJ | histidine/lysine/arginine/ornithine transporter permease subunit/histidine/lysine/arginine/ornithine transporter subunit |
| ? | CP009273 | 2419477 = | 99 (1.480) | intergenic (‑82/+8) | hisQ/hisJ | histidine/lysine/arginine/ornithine transporter permease subunit/histidine/lysine/arginine/ornithine transporter subunit | |||||
| * | ? | CP009273 | = 2509092 | NA (NA) | 3 (0.040) | 3/264 | NT | 3.2% | intergenic (+170/+30) | insL1/yfeA | IS186 transposase/putative diguanylate cyclase |
| ? | CP009273 | = 2595151 | 92 (1.320) | coding (592/618 nt) | hyfA | hydrogenase 4, 4Fe‑4S subunit | |||||
| * | ? | CP009273 | = 3051790 | 101 (1.440) | 8 (0.120) | 4/258 | NT | 7.4% | intergenic (‑21/+235) | serA/rpiA | D‑3‑phosphoglycerate dehydrogenase/ribose 5‑phosphate isomerase, constitutive |
| ? | CP009273 | = 3051827 | 103 (1.540) | intergenic (‑58/+198) | serA/rpiA | D‑3‑phosphoglycerate dehydrogenase/ribose 5‑phosphate isomerase, constitutive | |||||
| * | ? | CP009273 | = 4161824 | 57 (0.810) | 7 (0.110) | 4/254 | NT | 11.5% | intergenic (+140/‑161) | rrfB/murB | 5S ribosomal RNA of rrnB operon/UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding |
| ? | CP009273 | = 4161829 | NA (NA) | intergenic (+145/‑156) | rrfB/murB | 5S ribosomal RNA of rrnB operon/UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding | |||||
| * | ? | CP009273 | 4532499 = | 53 (0.760) | 4 (0.060) | 4/252 | NT | 7.8% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | CP009273 | 4532813 = | 45 (0.690) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | CP009273 | 4551364 = | 80 (1.140) | 4 (0.060) | 3/256 | NT | 5.6% | coding (1129/1179 nt) | yjiJ | DUF1228 family putative inner membrane MFS superfamily transporter |
| ? | CP009273 | 4551429 = | 60 (0.900) | coding (1064/1179 nt) | yjiJ | DUF1228 family putative inner membrane MFS superfamily transporter | |||||