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 | 121,435 | T→C | 7.2% | G644G (GGT→GGC) | aceE → | pyruvate dehydrogenase, decarboxylase component E1, thiamine triphosphate‑binding |
| RA | 190,047 | G→T | 11.9% | G14C (GGT→TGT) | dxr → | 1‑deoxy‑D‑xylulose 5‑phosphate reductoisomerase |
| RA | 254,371 | T→A | 11.9% | L19Q (CTA→CAA) | crl → | RNA polymerase holoenzyme assembly factor crl |
| RA | 353,289 | T→C | 10.7% | intergenic (+124/+213) | codA → / ← cynR | cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor |
| RA | 468,288 | A→T | 57.8% | K79* (AAG→TAG) | glnK → | nitrogen assimilation regulatory protein for GlnL, GlnE, and AmtB |
| RA | 571,240 | C→A | 53.3% | intergenic (‑31/+2) | insH1 ← / ← nmpC | IS5 transposase and trans‑activator/DLP12 prophage; truncated outer membrane porin (pseudogene);IS, phage, Tn; Phage or Prophage Related; outer membrane porin protein; locus of qsr prophage |
| RA | 717,068 | G→A | 9.4% | A41V (GCG→GTG) | kdpE ← | response regulator in two‑component regulatory system with KdpD |
| RA | 753,013 | G→T | 45.4% | E551* (GAA→TAA) | sdhA → | succinate dehydrogenase, flavoprotein subunit |
| RA | 761,379 | C→T | 8.4% | intergenic (‑48/‑61) | mngR ← / → mngA | Transcriptional repressor for the mannosyl‑D‑glycerate catabolic operon/fused 2‑O‑a‑mannosyl‑D‑glycerate specific PTS enzymes: IIA component/IIB component/IIC component |
| RA | 982,566 | C→A | 23.2% | intergenic (‑128/+475) | ompF ← / ← asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase |
| RA | 1,032,559 | C→T | 9.4% | R119W (CGG→TGG) | hyaF → | protein involved in nickel incorporation into hydrogenase‑1 proteins |
| RA | 1,144,365 | G→T | 34.4% | V51F (GTT→TTT) | fabH → | 3‑oxoacyl‑[acyl‑carrier‑protein] synthase III |
| RA | 1,236,056 | A→G | 7.2% | L491P (CTG→CCG) | cvrA ← | putative cation/proton antiporter |
| RA | 1,373,339 | G→A | 7.2% | R400H (CGC→CAC) | ycjT → | putative family 65 glycosyl hydrolase |
| RA | 1,469,323 | T→A | 8.4% | G282G (GGT→GGA) | ydbC → | putative NAD(P)‑binding oxidoreductase |
| RA | 1,572,548 | A→T | 11.5% | L351H (CTC→CAC) | yddA ← | putative multidrug transporter subunit of ABC superfamily, membrane component/ATP‑binding component |
| RA | 2,017,857 | T→C | 8.0% | S137P (TCA→CCA) | rcsA → | transcriptional regulator of colanic acid capsular biosynthesis |
| RA | 2,057,920 | G→A | 6.5% | T10M (ACG→ATG) | cobT ← | nicotinate‑nucleotide‑‑dimethylbenzimidazole phosphoribosyltransferase |
| RA | 2,083,335 | A→T | 9.8% | intergenic (‑141/‑142) | yefM ← / → hisL | antitoxin of the YoeB‑YefM toxin‑antitoxin system/his operon leader peptide |
| RA | 2,181,048 | T→C | 8.3% | P282P (CCA→CCG) | yehA ← | putative fimbrial‑like adhesin protein |
| RA | 2,299,755 | A→G | 5.9% | L160S (TTG→TCG) | mqo ← | malate dehydrogenase, FAD/NAD(P)‑binding domain |
| JC JC | 2,400,257 | IS5 (+) +4 bp | 73.8% | intergenic (‑137/‑780) | lrhA ← / → alaA | transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2 |
| RA | 2,420,353 | A→T | 67.3% | intergenic (‑86/+135) | hisJ ← / ← argT | histidine/lysine/arginine/ornithine transporter subunit/lysine/arginine/ornithine transporter subunit |
| JC | 2,420,942:1 | +CGT | 23.8% | coding (329/783 nt) | argT ← | lysine/arginine/ornithine transporter subunit |
| RA | 2,421,172 | A→C | 32.0% | D33E (GAT→GAG) | argT ← | lysine/arginine/ornithine transporter subunit |
| RA | 2,470,499 | T→A | 4.2% | R204* (AGA→TGA) | dsdC ← | dsd operon activator; autorepressor |
| RA | 2,592,650 | A→T | 5.8% | I157N (ATT→AAT) | dapA ← | dihydrodipicolinate synthase |
| RA | 2,717,970 | G→C | 9.4% | A379G (GCG→GGG) | kgtP ← | alpha‑ketoglutarate transporter |
| RA | 2,718,678 | C→G | 38.3% | G143A (GGC→GCC) | kgtP ← | alpha‑ketoglutarate transporter |
| RA | 2,719,426 | T→C | 38.8% | intergenic (‑321/+2) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,811,405 | A→G | 8.0% | intergenic (‑186/+13) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,859,846 | G→C | 4.4% | intergenic (+22/+72) | ygbN → / ← rpoS | putative transporter/RNA polymerase, sigma S (sigma 38) factor |
| RA | 2,859,847 | G→C | 4.6% | intergenic (+23/+71) | ygbN → / ← rpoS | putative transporter/RNA polymerase, sigma S (sigma 38) factor |
| RA | 2,861,917 | G→A | 36.1% | Q66* (CAG→TAG) | nlpD ← | activator of AmiC murein hydrolase activity, lipoprotein |
| RA | 2,870,339 | G→A | 37.7% | G134S (GGC→AGC) | iap → | aminopeptidase in alkaline phosphatase isozyme conversion |
| RA | 3,019,631 | G→T | 31.1% | M169I (ATG→ATT) | guaD → | guanine deaminase |
| RA | 3,029,079 | C→T | 38.2% | A188T (GCT→ACT) | prfB ← | peptide chain release factor RF‑2 |
| RA | 3,176,704:1 | +T | 6.5% | intergenic (+22/+468) | zupT → / ← ribB | zinc transporter/3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase |
| RA | 3,176,709 | Δ1 bp | 6.3% | intergenic (+27/+463) | zupT → / ← ribB | zinc transporter/3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase |
| JC JC | 3,178,254 | IS5 (+) +4 bp | 74.0% | coding (56‑59/291 nt) | yqiC → | BMFP family putative fusogenic protein |
| RA | 3,341,024 | G→A | 9.6% | R184H (CGC→CAC) | yhbJ → | adaptor protein RapZ for GlmZ/GlmY sRNA decay; glucosamine‑6‑phosphate regulated; NTPase |
| RA | 3,706,647 | G→T | 28.7% | V66L (GTG→TTG) | tag → | 3‑methyl‑adenine DNA glycosylase I, constitutive |
| RA | 3,787,229 | T→C | 7.5% | intergenic (‑186/‑118) | yibB ← / → hldD | YibB family protein, function unknown/ADP‑L‑glycero‑D‑mannoheptose‑6‑epimerase, NAD(P)‑binding |
| RA | 3,856,737 | G→A | 10.2% | pseudogene (227/1617 nt) | glvC ← | pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component |
| RA | 3,960,789 | C→G | 18.3% | T338R (ACA→AGA) | rho → | transcription termination factor |
| RA | 4,049,411 | G→T | 14.8% | Q97K (CAG→AAG) | glnL ← | sensory histidine kinase in two‑component regulatory system with GlnG |
| JC | 4,108,819:1 | +TGT | 5.4% | coding (440/486 nt) | rraA ← | ribonuclease E (RNase E) inhibitor protein |
| RA | 4,125,862 | C→T | 7.3% | S700S (AGC→AGT) | katG → | catalase‑peroxidase HPI, heme b‑containing |
| RA | 4,234,563 | G→A | 9.5% | D147D (GAC→GAT) | malF ← | maltose transporter subunit |
| RA | 4,297,722 | A→T | 8.7% | F192I (TTT→ATT) | alsE ← | allulose‑6‑phosphate 3‑epimerase |
| RA | 4,390,205 | G→T | 60.3% | G34V (GGG→GTG) | hfq → | global sRNA chaperone; HF‑I, host factor for RNA phage Q beta replication |
| RA | 4,475,797 | C→T | 8.2% | intergenic (‑29/‑238) | pepA ← / → lptF | multifunctional aminopeptidase A: a cyteinylglycinase, transcription regulator and site‑specific recombination factor/lipopolysaccharide export ABC permease of the LptBFGC export complex |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 19796 = | NA (NA) | 10 (0.200) | 10/276 | NT | 21.7% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | CP009273 | 3649844 = | 36 (0.720) | coding (257/333 nt) | hdeA | stress response protein acid‑resistance protein | |||||
| * | ? | CP009273 | 310940 = | 52 (1.040) | 7 (0.140) +TC |
7/272 | NT | 10.3% | intergenic (+1/‑62) | eaeH/insE1 | pseudogene, attaching and effacing protein homology;factor; Not classified/IS3 transposase A |
| ? | CP009273 | 642345 = | 72 (1.450) | coding (621/879 nt) | citG | 2‑(5''‑triphosphoribosyl)‑3'‑dephosphocoenzyme‑A synthase | |||||
| * | ? | CP009273 | = 312194 | NA (NA) | 9 (0.180) | 8/276 | NT | 11.0% | intergenic (+30/+3) | insF1/ykgA | IS3 transposase B/pseudogene, AraC family;putative regulator; Not classified; putative ARAC‑type regulatory protein |
| ? | CP009273 | = 642348 | 73 (1.470) | coding (618/879 nt) | citG | 2‑(5''‑triphosphoribosyl)‑3'‑dephosphocoenzyme‑A synthase | |||||
| * | ? | CP009273 | 360104 = | NA (NA) | 62 (1.250) | 46/276 | 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 | 1203246 = | 18 (0.360) | 28 (0.640) | 23/244 | NT | 64.4% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 15 (0.340) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 16 (0.320) | 29 (0.660) | 24/244 | NT | 66.6% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 15 (0.340) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1391495 | NA (NA) | 19 (0.380) | 17/276 | NT | 65.5% | intergenic (+146/‑127) | insH1/ynaJ | IS5 transposase and trans‑activator/DUF2534 family putative inner membrane protein |
| ? | CP009273 | = 1972751 | 10 (0.200) | intergenic (‑297/‑483) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein | |||||
| * | ? | CP009273 | = 1463497 | NA (NA) | 10 (0.200) | 9/272 | NT | 21.7% | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | CP009273 | = 1584819 | 36 (0.730) | intergenic (‑26/+292) | yneL/hipA | pseudogene, AraC family/inactivating GltX kinase facilitating persister formation; toxin of HipAB TA pair; autokinase | |||||
| * | ? | CP009273 | 1584814 = | 36 (0.720) | 4 (0.080) | 4/274 | NT | 10.1% | intergenic (‑21/+297) | yneL/hipA | pseudogene, AraC family/inactivating GltX kinase facilitating persister formation; toxin of HipAB TA pair; autokinase |
| ? | CP009273 | = 1645804 | NA (NA) | intergenic (+10/‑4) | insD1/intQ | IS2 transposase TnpB;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related/pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related | |||||
| * | ? | CP009273 | 1972748 = | 10 (0.200) | 23 (0.470) | 15/274 | NT | 69.7% | 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 (0.400) | 23 (0.460) | 18/276 | NT | 53.5% | 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 | 20 (0.400) | 22 (0.440) | 19/276 | NT | 52.4% | 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 | 2323869 = | 84 (1.690) | 3 (0.060) | 3/258 | NT | 3.8% | pseudogene (4013/4605 nt) | yfaS | pseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein |
| ? | CP009273 | 2323928 = | 74 (1.590) | pseudogene (3954/4605 nt) | yfaS | pseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein | |||||
| * | ? | CP009273 | 2991102 = | 72 (1.450) | 3 (0.060) | 3/262 | NT | 4.2% | pseudogene (1086/1137 nt) | ygeQ | pseudogene |
| ? | CP009273 | 2991140 = | 69 (1.460) | pseudogene (1048/1137 nt) | ygeQ | pseudogene | |||||
| * | ? | CP009273 | 3559560 = | 28 (0.560) | 3 (0.060) | 3/274 | NT | 8.5% | coding (382/2448 nt) | glgP | glycogen phosphorylase |
| ? | CP009273 | 3559591 = | 37 (0.750) | coding (351/2448 nt) | glgP | glycogen phosphorylase | |||||
| * | ? | CP009273 | 4532499 = | 32 (0.640) | 6 (0.130) | 4/258 | NT | 16.7% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | CP009273 | 4532813 = | 30 (0.650) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||