mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | CP000731 | 81 | N→G | 100% | intergenic (–/‑151) | – / → repA | –/replication protein A |
| JC | CP000731 | 6,552 | +28 bp | 100% | intergenic (+1069/‑419) | cadX → / → USA300HOU_pUSA300HOUMR0010 | cadmium efflux regulator/MarR family transcriptional regulator |
| RA | CP000731 | 21,093 | A→T | 5.6% | intergenic (‑23/‑451) | USA300HOU_pUSA300HOUMR0027 ← / → USA300HOU_pUSA300HOUMR0028 | IS431mec transposase/macrolide transporter |
| RA | CP000731 | 25,663 | Δ1 bp | 100% | coding (316/333 nt) | USA300HOU_pUSA300HOUMR0031 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 72,351 | A→G | 5.9% | L208S (TTA→TCA) | arcD_1 ← | Arginine/ornithine antiporter |
| RA | USA300TCH1516_ALE | 111,512 | A→G | 28.0% | S194S (TCA→TCG) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,516 | C→A | 26.2% | Q196K (CAA→AAA) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,560 | T→C | 8.2% | R210R (CGT→CGC) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 512,643 | A→G | 52.9% | intergenic (+711/‑6052) | recR → / → speA_2 | Recombination protein RecR/Arginine decarboxylase |
| RA | USA300TCH1516_ALE | 873,632 | A→T | 6.0% | S179S (TCA→TCT) | clfA → | Clumping factor A |
| RA | USA300TCH1516_ALE | 906,978 | C→T | 6.9% | intergenic (+87/‑342) | USA300HOU_RS04490 → / → USA300HOU_RS04495 | hypothetical protein/hypothetical protein |
| RA | USA300TCH1516_ALE | 984,359 | A→G | 5.9% | K101E (AAA→GAA) | USA300HOU_RS04865 → | 65 kDa membrane protein |
| RA | USA300TCH1516_ALE | 1,056,257 | C→A | 12.8% | intergenic (‑76/+120) | patA_2 ← / ← mdoC | Putative N‑acetyl‑LL‑diaminopimelate aminotransferase/Glucans biosynthesis protein C |
| RA | USA300TCH1516_ALE | 1,081,153 | T→C | 6.8% | N295N (AAT→AAC) | purM → | Phosphoribosylformylglycinamidine cyclo‑ligase |
| RA | USA300TCH1516_ALE | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | oppD_4 ← | Oligopeptide transport ATP‑binding protein OppD |
| RA | USA300TCH1516_ALE | 1,513,930 | A→T | 100% | L413F (TTA→TTT) | USA300HOU_RS07375 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | ypdF ← | Aminopeptidase YpdF |
| RA | USA300TCH1516_ALE | 1,744,362 | G→A | 11.1% | H104Y (CAC→TAC) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,744,424 | A→G | 10.0% | L83S (TTA→TCA) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,744,473 | C→T | 8.0% | A67T (GCT→ACT) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,744,644 | C→A | 22.8% | V10F (GTT→TTT) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,857,839 | T→C | 7.0% | I179V (ATT→GTT) | USA300HOU_RS09235 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,857,867 | C→T | 7.9% | L169L (TTG→TTA) | USA300HOU_RS09235 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | USA300HOU_RS10125 ← | Putative multidrug export ATP‑binding/permease protein |
| RA | USA300TCH1516_ALE | 2,233,544 | T→C | 6.5% | E174G (GAA→GGA) | prmC ← | Release factor glutamine methyltransferase |
| RA | USA300TCH1516_ALE | 2,279,705 | G→A | 100% | A943V (GCA→GTA) | ebh_3 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 2,386,969 | A→T | 6.9% | K117* (AAA→TAA) | USA300HOU_RS12255 → | putative HTH‑type transcriptional regulator |
| RA | USA300TCH1516_ALE | 2,390,270 | T→C | 7.3% | E54G (GAA→GGA) | moaA ← | GTP 3',8‑cyclase |
| RA | USA300TCH1516_ALE | 2,519,951 | T→G | 6.5% | P227P (CCA→CCC) | narG ← | Respiratory nitrate reductase 1 alpha chain |
| RA | USA300TCH1516_ALE | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
| RA | USA300TCH1516_ALE | 2,698,922 | T→C | 6.5% | R745R (CGT→CGC) | copA → | Copper‑exporting P‑type ATPase A |
| RA | USA300TCH1516_ALE | 2,774,981 | A→G | 9.7% | D735D (GAT→GAC) | clfB ← | Clumping factor B |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | = 260294 | 49 (0.770) | 3 (0.050) | 3/238 | NT | 6.1% | intergenic (‑408/‑180) | potD_1/pflB | Spermidine/putrescine‑binding periplasmic protein/Formate acetyltransferase |
| ? | USA300TCH1516_ALE | = 260312 | 48 (0.820) | intergenic (‑426/‑162) | potD_1/pflB | Spermidine/putrescine‑binding periplasmic protein/Formate acetyltransferase | |||||
| * | ? | USA300TCH1516_ALE | 512620 = | 61 (0.960) | 54 (1.230) +40 bp |
45/180 | NT | 56.2% | intergenic (+688/‑6075) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| ? | USA300TCH1516_ALE | 1998278 = | NA (NA) | intergenic (‑6/+3329) | USA300TCH1516_01882/USA300TCH1516_01883 | tRNA‑Val/tRNA‑Ala | |||||
| * | ? | USA300TCH1516_ALE | = 1205323 | 62 (0.970) | 3 (0.050) +AGCGAA |
3/248 | NT | 6.3% | intergenic (‑204/‑365) | USA300HOU_RS15290/lspA | hypothetical protein/Lipoprotein signal peptidase |
| ? | USA300TCH1516_ALE | = 1893309 | 32 (0.500) | intergenic (‑170/+177) | USA300TCH1516_01750/ytpA | hypothetical protein/Phospholipase YtpA | |||||
| * | ? | USA300TCH1516_ALE | 2001491 = | 7 (0.110) | 6 (0.100) | 4/246 | NT | 47.5% | intergenic (‑3219/+116) | USA300TCH1516_01882/USA300TCH1516_01883 | tRNA‑Val/tRNA‑Ala |
| ? | USA300TCH1516_ALE | 2179606 = | NA (NA) | intergenic (+3368/+1927) | ilvA/USA300TCH1516_02069 | L‑threonine dehydratase biosynthetic IlvA/tRNA‑Gly | |||||