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 | 25,865 | C→T | 10.8% | H14Y (CAC→TAC) | fkpB → | FKBP‑type peptidyl‑prolyl cis‑trans isomerase (rotamase) |
| RA | 966,112 | A→T | 12.2% | intergenic (+35/‑17) | ycaQ → / → ycaR | DUF1006 family protein with C‑terminal wHTH domain/peroxide and acid resistance protein, UPF0434 family |
| RA | 1,804,319 | T→C | 12.1% | intergenic (+14/‑149) | yniC → / → ydjM | 2‑deoxyglucose‑6‑P phosphatase/inner membrane protein regulated by LexA |
| RA | 2,270,615 | A→G | 29.4% | E279E (GAA→GAG) | yejF → | microcin C transporter, ATP‑binding subunit; ABC family |
| JC JC | 2,400,257 | IS5 (+) +4 bp | 50.8% | intergenic (‑137/‑780) | lrhA ← / → alaA | transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2 |
| RA | 2,419,720 | T→C | 43.2% | D183G (GAT→GGT) | hisJ ← | histidine/lysine/arginine/ornithine transporter subunit |
| RA | 2,419,933 | G→T | 45.4% | A112D (GCC→GAC) | hisJ ← | histidine/lysine/arginine/ornithine transporter subunit |
| RA | 2,420,328 | G→A | 52.9% | intergenic (‑61/+160) | hisJ ← / ← argT | histidine/lysine/arginine/ornithine transporter subunit/lysine/arginine/ornithine transporter subunit |
| RA | 2,420,329 | C→A | 53.2% | intergenic (‑62/+159) | hisJ ← / ← argT | histidine/lysine/arginine/ornithine transporter subunit/lysine/arginine/ornithine transporter subunit |
| JC | 2,420,338:1 | +AATT | 51.8% | intergenic (‑71/+150) | hisJ ← / ← argT | histidine/lysine/arginine/ornithine transporter subunit/lysine/arginine/ornithine transporter subunit |
| JC JC | 3,178,254 | IS5 (+) +4 bp | 76.7% | coding (56‑59/291 nt) | yqiC → | BMFP family putative fusogenic protein |
| RA | 3,178,277 | G→T | 21.1% | E27* (GAA→TAA) | yqiC → | BMFP family putative fusogenic protein |
| RA | 3,196,981 | C→A | 8.7% | P170P (CCG→CCT) | bacA ← | undecaprenyl pyrophosphate phosphatase |
| RA | 3,883,195 | C→T | 12.1% | P369L (CCG→CTG) | tnaA → | tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent |
| RA | 3,953,437 | Δ1 bp | 67.6% | pseudogene (178/243 nt) | yifN ← | PemK toxin family pseudogene |
| RA | 3,969,337 | G→T | 49.7% | E278* (GAG→TAG) | wecE → | TDP‑4‑oxo‑6‑deoxy‑D‑glucose transaminase |
| RA | 4,049,665 | A→C | 31.8% | I12S (ATC→AGC) | glnL ← | sensory histidine kinase in two‑component regulatory system with GlnG |
| RA | 4,113,470 | C→T | 10.5% | R305R (CGG→CGA) | cytR ← | Anti‑activator for CytR‑CRP nucleoside utilization regulon |
| RA | 4,546,084 | G→T | 24.0% | H18Q (CAC→CAA) | yjiC ← | uncharacterized protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | = 350323 | 34 (1.180) | 3 (0.110) | 3/256 | NT | 8.3% | noncoding (14/171 nt) | REP26 (repetitive extragenic palindromic) element; contains 4 REP sequences | REP26 (repetitive extragenic palindromic) element; contains 4 REP sequences |
| ? | CP009273 | = 350357 | 34 (1.250) | noncoding (48/171 nt) | REP26 (repetitive extragenic palindromic) element; contains 4 REP sequences | REP26 (repetitive extragenic palindromic) element; contains 4 REP sequences | |||||
| * | ? | CP009273 | 360104 = | NA (NA) | 49 (1.710) | 40/270 | 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 | = 1046001 | 22 (0.770) | 14 (0.490) | 13/270 | NT | 40.6% | intergenic (+15/+418) | insB1/cspH | IS1 transposase B/stress protein, member of the CspA‑family |
| ? | CP009273 | 1973060 = | 19 (0.660) | intergenic (‑606/‑174) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein | |||||
| * | ? | CP009273 | = 1203261 | 27 (0.940) | 6 (0.240) | 3/238 | NT | 16.7% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 36 (1.420) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | 1390301 = | NA (NA) | 7 (0.240) | 7/270 | NT | 29.2% | intergenic (‑122/‑32) | ynaI/insH1 | mechanosensitive channel protein, very small conductance/IS5 transposase and trans‑activator |
| ? | CP009273 | = 1539172 | 17 (0.590) | pseudogene (800/951 nt) | yddK | pseudogene, leucine‑rich protein; putative glycoportein | |||||
| * | ? | CP009273 | = 1401356 | 30 (1.040) | 120 (4.180) | 83/270 | NT | 80.0% | coding (697/1233 nt) | ydaM | diguanylate cyclase, csgD regulator |
| ? | CP009273 | = 2283592 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | CP009273 | = 1973068 | 17 (0.590) | 9 (0.310) | 8/270 | NT | 34.6% | intergenic (‑614/‑166) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein |
| ? | CP009273 | 3576788 = | NA (NA) | intergenic (+10/‑55) | yrhA/insA | pseudogene, interrupted by IS1E/IS1 repressor TnpA | |||||
| * | ? | CP009273 | = 3180785 | NA (NA) | 8 (0.280) | 6/270 | NT | 36.4% | pseudogene (6/2445 nt) | yqiG | pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein |
| ? | CP009273 | 3710988 = | 14 (0.490) | coding (319/975 nt) | ghrB | glyoxylate/hydroxypyruvate reductase B | |||||
| * | ? | CP009273 | = 3360109 | NA (NA) | 7 (0.240) | 6/270 | NT | 28.0% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | CP009273 | 3371007 = | 18 (0.630) | intergenic (‑228/+167) | sspA/rpsI | stringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog/30S ribosomal subunit protein S9 | |||||
| * | ? | CP009273 | = 3710992 | 14 (0.490) | 8 (0.280) | 8/270 | NT | 36.4% | coding (323/975 nt) | ghrB | glyoxylate/hydroxypyruvate reductase B |
| ? | CP009273 | 4487998 = | NA (NA) | intergenic (+241/‑91) | intB/insC1 | pseudogene, integrase homology;IS, phage, Tn; Phage‑related functions and prophages; KpLE2 phage‑like element; P4‑like integrase/IS2 repressor TnpA | |||||
| * | ? | CP009273 | = 4117974 | NA (NA) | 9 (0.330) | 9/256 | NT | 32.1% | noncoding (95/97 nt) | RIP305 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP305 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | CP009273 | 4121055 = | 19 (0.700) | coding (1293/2433 nt) | metL | Bifunctional aspartokinase/homoserine dehydrogenase 2 | |||||