mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.32.0 revision 6ff6de7d1b87
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| JC | 66,614 | Δ170 bp | 2.9% | intergenic (‑64/+52) | araD ← / ← araA | L‑ribulose‑5‑phosphate 4‑epimerase/L‑arabinose isomerase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 417,602 | A→G | 3.5% | E154G (GAG→GGG) | phoB → | response regulator in two‑component regulatory system with PhoR |
| RA | 523,618 | A→G | 13.5% | S120G (AGC→GGC) | rhsD → | Rhs protein with DUF4329 family putative toxin domain, putative neighboring cell growth inhibitor |
| RA | 548,918 | Δ1 bp | 2.8% | coding (562/1260 nt) | ylbE → | NO‑induced DUF1116 protein |
| JC | 723,107 | (CAC)4→3 | 2.8% | coding (1306‑1308/2685 nt) | kdpD ← | fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein |
| RA | 808,319 | Δ1 bp | 3.1% | coding (939/1290 nt) | bioA ← | 7,8‑diaminopelargonic acid synthase, PLP‑dependent |
| RA | 898,041 | G→A | 3.0% | R18H (CGC→CAC) | ybjO → | DUF2593 family inner membrane protein |
| RA | 937,515 | T→A | 2.6% | G48G (GGT→GGA) | lolA → | lipoprotein chaperone |
| RA | 965,195 | A→T | 3.4% | G292G (GGA→GGT) | ycaI → | ComEC family inner membrane protein |
| RA | 989,368 | G→A | 4.1% | S330F (TCC→TTC) | pncB ← | nicotinate phosphoribosyltransferase |
| RA | 1,061,011:1 | +G | 3.1% | coding (1756/2547 nt) | torA → | trimethylamine N‑oxide (TMAO) reductase I, catalytic subunit |
| RA | 1,135,049 | G→A | 2.8% | L107L (TTG→TTA) | flgG → | flagellar component of cell‑distal portion of basal‑body rod |
| RA | 1,475,189 | T→A | 3.4% | F16I (TTT→ATT) | ydbD → | PF10971 family putative periplasmic methylglyoxal resistance protein |
| RA | 1,728,327 | Δ1 bp | 4.0% | intergenic (+83/‑20) | gloA → / → rnt | glyoxalase I, Ni‑dependent/RNase T, exoribonuclease T, structured DNA 3' exonuclease, RNA processing, DNA repair |
| RA | 1,739,613 | T→C | 9.6% | G62G (GGA→GGG) | ydhB ← | LysR family putative transcriptional regulator |
| RA | 1,787,100 | C→T | 7.2% | G5S (GGC→AGC) | ppsA ← | phosphoenolpyruvate synthase |
| RA | 1,823,120 | G→A | 3.6% | L221L (CTG→CTA) | nadE → | NAD synthetase, NH3/glutamine‑dependent |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,399,731 | A→G | 5.8% | S145P (TCT→CCT) | nuoG ← | NADH:ubiquinone oxidoreductase, chain G |
| RA | 2,428,375:1 | +T | 3.1% | coding (250/570 nt) | ubiX ← | 3‑octaprenyl‑4‑hydroxybenzoate carboxy‑lyase |
| RA | 2,662,949 | A→T | 3.2% | L125M (TTG→ATG) | trmJ ← | tRNA mC32,mU32 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 2,785,699 | T→C | 3.0% | intergenic (‑690/+61) | ypjC ← / ← ileY | pseudogene/tRNA‑Ile |
| RA | 3,232,250 | Δ1 bp | 2.6% | coding (588/2019 nt) | fadH → | 2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked |
| RA | 3,653,294 | A→T | 4.1% | pseudogene (65/483 nt) | yhiS → | pseudogene |
| RA | 3,688,286 | A→C | 10.3% | V296G (GTG→GGG) | bcsC ← | cellulose synthase subunit |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,875,524 | G→T | 8.3% | V30F (GTT→TTT) | yidX → | putative lipoprotein |
| RA | 3,879,028 | T→G | 6.9% | N364T (AAC→ACC) | gyrB ← | DNA gyrase, subunit B |
| RA | 3,983,192 | T→C | 5.9% | L79P (CTC→CCC) | aslB → | putative AslA‑specific sulfatase‑maturating enzyme |
| MC JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,004,531 | G→T | 5.0% | Q56K (CAA→AAA) | yigI ← | 4HBT thioesterase family protein |
| RA | 4,096,634 | T→A | 2.5% | T272S (ACC→TCC) | rhaB ← | rhamnulokinase |
| RA | 4,152,403 | A→G | 4.7% | L232P (CTC→CCC) | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,203,890 | A→G | 2.6% | K191R (AAA→AGA) | zraR → | fused DNA‑binding response regulator in two‑component regulatory system with ZraS: response regulator/sigma54 interaction protein |
| RA | 4,229,994 | T→A | 2.8% | T50S (ACA→TCA) | pepE ← | peptidase E, alpha‑aspartyl dipeptidase |
| RA | 4,275,067 | Δ1 bp | 2.7% | intergenic (‑27/‑403) | yjcB ← / → yjcC | putative inner membrane protein/putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase |
| RA | 4,296,189 | A→G | 11.5% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 13.7% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,336,125 | G→A | 3.7% | A303V (GCC→GTC) | adiC ← | arginine:agmatine antiporter |
| RA | 4,571,695 | T→A | 3.6% | intergenic (‑120/‑57) | yjiR ← / → yjiS | putative DNA‑binding transcriptional regulator/putative aminotransferase/DUF1127 family protein |
| RA | 4,614,322 | A→G | 3.9% | intergenic (+61/+359) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| RA | 4,614,323 | A→T | 4.3% | intergenic (+62/+358) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| RA | 4,614,448 | C→T | 6.0% | intergenic (+187/+233) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423900–3424232 | 3424387–3424236 | 5–488 | 25 [20] | [22] 24 | rrlD | 23S ribosomal RNA of rrnD operon |
| * | * | ÷ | NC_000913 | 4233780 | 4235386 | 1607 | 25 [18] | [23] 25 | pgi | glucosephosphate isomerase |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 120 (0.800) | 72/460 | NT | 99.2% | intergenic (+9/‑768) | crl/crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers |
| ? | NC_000913 | = 1293039 | 1 (0.010) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | = 832060 | 114 (0.760) | 3 (0.020) | 3/446 | NT | 3.0% | coding (1189/1365 nt) | rhlE | ATP‑dependent RNA helicase |
| ? | NC_000913 | = 832200 | 84 (0.580) | coding (1329/1365 nt) | rhlE | ATP‑dependent RNA helicase | |||||
| * | ? | NC_000913 | 1207790 = | 18 (0.120) | 99 (0.710) | 60/428 | NT | 86.6% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 14 (0.100) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 18 (0.120) | 113 (0.810) | 68/428 | NT | 88.0% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 14 (0.100) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 2 (0.010) | 106 (0.710) | 71/460 | NT | 98.1% | intergenic (‑110/‑495) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| ? | NC_000913 | = 1979270 | NA (NA) | intergenic (‑55/‑483) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 47 (0.320) | 38/452 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 83 (0.570) | 59/444 | NT | 100% | intergenic (‑305/+16) | flhD/insB1 | flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B |
| ? | NC_000913 | 1979279 = | 0 (0.000) | intergenic (‑64/‑474) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 57 (0.380) | 40/460 | NT | 100% | intergenic (‑271/‑267) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | 2101749 = | NA (NA) | intergenic (‑5/+146) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | = 1979489 | 0 (0.000) | 117 (0.780) | 67/460 | NT | 100% | intergenic (‑274/‑264) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | = 2290111 | NA (NA) | intergenic (‑32/+1) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system | |||||
| * | ? | NC_000913 | 2304885 = | 66 (0.440) | 20 (0.130) | 7/454 | NT | 21.1% | noncoding (471/655 nt) | REP161 (repetitive extragenic palindromic) element, contains 12 REP sequences | REP161 (repetitive extragenic palindromic) element, contains 12 REP sequences |
| ? | NC_000913 | = 4296263 | 84 (0.570) | noncoding (430/602 nt) | RIP321 (repetitive extragenic palindromic) element, contains 11 REP sequences and 4 IHF sites | RIP321 (repetitive extragenic palindromic) element, contains 11 REP sequences and 4 IHF sites | |||||
| * | ? | NC_000913 | = 3427075 | 17 (0.110) | 4 (0.030) | 4/442 | NT | 7.9% | noncoding (76/77 nt) | ileU | tRNA‑Ile |
| ? | NC_000913 | 4037236 = | 77 (0.530) | intergenic (+20/‑23) | ileT/alaT | tRNA‑Ile/tRNA‑Ala | |||||