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 | 15,413 | C→T | 13.8% | D68N (GAC→AAC) | USA300HOU_pUSA300HOUMR0019 ← | strepthothricin acetyltransferase |
| RA | CP000731 | 25,663 | Δ1 bp | 100% | coding (316/333 nt) | USA300HOU_pUSA300HOUMR0031 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 110,651 | C→T | 14.0% | D170D (GAC→GAT) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 110,660 | T→A | 21.2% | I173I (ATT→ATA) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,512 | A→G | 31.5% | S194S (TCA→TCG) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,516 | C→A | 30.7% | Q196K (CAA→AAA) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,560 | T→C | 11.3% | R210R (CGT→CGC) | USA300HOU_RS00520 → | putative lipoprotein |
| JC | USA300TCH1516_ALE | 130,854 | (T)5→1 | 14.4% | intergenic (‑94/+272) | sarS ← / ← yfhA | HTH‑type transcriptional regulator SarS/putative siderophore transport system permease protein YfhA |
| RA | USA300TCH1516_ALE | 512,643 | A→G | 54.5% | intergenic (+711/‑6052) | recR → / → speA_2 | Recombination protein RecR/Arginine decarboxylase |
| RA | USA300TCH1516_ALE | 590,688 | G→A | 5.4% | G302S (GGT→AGT) | rpoC → | DNA‑directed RNA polymerase subunit beta' |
| RA | USA300TCH1516_ALE | 622,533 | T→C | 17.4% | D1032D (GAT→GAC) | sdrE → | Serine‑aspartate repeat‑containing protein E |
| RA | USA300TCH1516_ALE | 849,017 | C→T | 17.5% | P48L (CCT→CTT) | USA300HOU_RS04145 → | Nucleotide‑binding protein |
| RA | USA300TCH1516_ALE | 1,097,015 | T→C | 7.4% | M270T (ATG→ACG) | ythB → | Putative cytochrome bd menaquinol oxidase subunit II |
| 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 | 1,892,051 | A→T | 20.9% | intergenic (‑144/+376) | rot ← / ← USA300TCH1516_01749 | HTH‑type transcriptional regulator rot/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 | 2,028,508 | A→T | 22.2% | V46E (GTA→GAA) | USA300HOU_RS10230 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,154,656 | A→G | 6.2% | F341L (TTT→CTT) | nrgA ← | Ammonium transporter NrgA |
| RA | USA300TCH1516_ALE | 2,211,305 | A→G | 24.9% | intergenic (+298/+515) | USA300HOU_RS11275 → / ← yidC | hypothetical protein/Membrane protein insertase YidC |
| RA | USA300TCH1516_ALE | 2,279,705 | G→A | 100% | A943V (GCA→GTA) | ebh_3 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 2,328,291 | G→A | 6.4% | A458V (GCA→GTA) | lacE ← | PTS system lactose‑specific EIICB component |
| RA | USA300TCH1516_ALE | 2,372,586 | G→T | 19.5% | S397* (TCA→TAA) | pbuG ← | Guanine/hypoxanthine permease PbuG |
| RA | USA300TCH1516_ALE | 2,373,715 | C→A | 9.8% | G21C (GGT→TGT) | pbuG ← | Guanine/hypoxanthine permease PbuG |
| RA | USA300TCH1516_ALE | 2,373,809 | A→T | 15.4% | intergenic (‑34/+79) | pbuG ← / ← topB | Guanine/hypoxanthine permease PbuG/DNA topoisomerase 3 |
| RA | USA300TCH1516_ALE | 2,504,989 | T→C | 10.3% | intergenic (+293/+111) | USA300HOU_RS12890 → / ← gltT | hypothetical protein/Proton/sodium‑glutamate symport protein |
| RA | USA300TCH1516_ALE | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
| RA | USA300TCH1516_ALE | 2,726,142 | A→G | 6.3% | Y48H (TAT→CAT) | USA300HOU_RS14025 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,755,876 | C→T | 5.4% | A202T (GCG→ACG) | opuD_3 ← | Glycine betaine transporter OpuD |
| RA | USA300TCH1516_ALE | 2,774,993 | A→G | 14.4% | D731D (GAT→GAC) | clfB ← | Clumping factor B |
| RA | USA300TCH1516_ALE | 2,775,041 | A→G | 13.3% | D715D (GAT→GAC) | clfB ← | Clumping factor B |
| RA | USA300TCH1516_ALE | 2,860,200 | C→T | 5.5% | R211C (CGT→TGT) | bceA_2 → | Bacitracin export ATP‑binding protein BceA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | 512620 = | 54 (0.960) | 40 (1.030) +40 bp |
28/178 | NT | 51.9% | 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 | |||||