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 | 25,663 | Δ1 bp | 100% | coding (316/333 nt) | USA300HOU_pUSA300HOUMR0031 → | hypothetical protein |
| RA | CP000731 | 26,652 | C→T | 5.6% | D66N (GAC→AAC) | USA300HOU_pUSA300HOUMR0033 ← | partitioning protein |
| RA | USA300TCH1516_ALE | 110,660 | T→A | 9.5% | I173I (ATT→ATA) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,330 | C→A | 6.8% | Q134K (CAA→AAA) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,512 | A→G | 30.3% | S194S (TCA→TCG) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,516 | C→A | 31.5% | Q196K (CAA→AAA) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,560 | T→C | 10.0% | R210R (CGT→CGC) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 156,752 | T→C | 5.3% | intergenic (‑32/‑219) | treR_1 ← / → deoD | HTH‑type transcriptional regulator TreR/Purine nucleoside phosphorylase DeoD‑type |
| RA | USA300TCH1516_ALE | 512,643 | A→G | 54.4% | intergenic (+711/‑6052) | recR → / → speA_2 | Recombination protein RecR/Arginine decarboxylase |
| RA | USA300TCH1516_ALE | 587,957 | G→T | 11.5% | A621S (GCG→TCG) | rpoB → | DNA‑directed RNA polymerase subunit beta |
| RA | USA300TCH1516_ALE | 787,902 | G→A | 5.5% | R23H (CGC→CAC) | USA300HOU_RS03860 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 937,148 | T→C | 5.0% | intergenic (+55/‑76) | USA300HOU_RS04665 → / → pepA_1 | NADH dehydrogenase‑like protein/Cytosol aminopeptidase |
| RA | USA300TCH1516_ALE | 937,158 | T→A | 5.3% | intergenic (+65/‑66) | USA300HOU_RS04665 → / → pepA_1 | NADH dehydrogenase‑like protein/Cytosol aminopeptidase |
| RA | USA300TCH1516_ALE | 937,168 | G→A | 5.3% | intergenic (+75/‑56) | USA300HOU_RS04665 → / → pepA_1 | NADH dehydrogenase‑like protein/Cytosol aminopeptidase |
| RA | USA300TCH1516_ALE | 1,035,144 | C→T | 6.2% | intergenic (‑66/‑133) | USA300TCH1516_00961 ← / → USA300TCH1516_00962 | Lipoate‑‑protein ligase 1/hypothetical protein |
| RA | USA300TCH1516_ALE | 1,117,630 | C→T | 8.1% | M1M (ATG→ATA) † | USA300TCH1516_01040 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,141,228 | G→A | 10.4% | E283K (GAA→AAA) | USA300HOU_RS05655 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,231,407 | G→A | 6.5% | E18K (GAA→AAA) | stp → | Serine/threonine phosphatase stp |
| RA | USA300TCH1516_ALE | 1,231,446 | C→T | 6.6% | Q31* (CAA→TAA) | stp → | Serine/threonine phosphatase stp |
| RA | USA300TCH1516_ALE | 1,400,393 | C→T | 6.1% | P73L (CCA→CTA) | dinB1 → | DNA polymerase IV 1 |
| RA | USA300TCH1516_ALE | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | oppD_4 ← | Oligopeptide transport ATP‑binding protein OppD |
| RA | USA300TCH1516_ALE | 1,433,870 | A→G | 10.7% | D287G (GAC→GGC) | dapA → | 4‑hydroxy‑tetrahydrodipicolinate synthase |
| RA | USA300TCH1516_ALE | 1,472,896 | T→C | 7.0% | K9710E (AAG→GAG) | ebh_1 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 1,507,931 | C→T | 6.7% | intergenic (‑356/+119) | ald1 ← / ← ypcP | Alanine dehydrogenase 1/5'‑3' exonuclease |
| RA | USA300TCH1516_ALE | 1,512,413 | A→G | 6.0% | intergenic (‑25/‑279) | USA300HOU_RS07370 ← / → USA300HOU_RS07375 | Bacterial dynamin‑like protein/hypothetical protein |
| RA | USA300TCH1516_ALE | 1,513,930 | A→T | 100% | L413F (TTA→TTT) | USA300HOU_RS07375 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,589,223 | A→G | 7.7% | V753V (GTT→GTC) | USA300HOU_RS07800 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | ypdF ← | Aminopeptidase YpdF |
| RA | USA300TCH1516_ALE | 1,673,843 | T→C | 6.1% | K391K (AAA→AAG) | dnaG ← | DNA primase |
| RA | USA300TCH1516_ALE | 1,744,443 | C→A | 16.7% | V77F (GTT→TTT) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,744,446 | G→A | 7.8% | P76S (CCT→TCT) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,744,544 | T→C | 44.4% | Y43C (TAC→TGC) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,781,307 | T→C | 5.1% | K471E (AAG→GAG) | lysP_2 ← | Lysine‑specific permease |
| RA | USA300TCH1516_ALE | 1,815,180 | T→C | 8.8% | E21G (GAA→GGA) | dnaE ← | DNA polymerase III subunit alpha |
| RA | USA300TCH1516_ALE | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | USA300HOU_RS10125 ← | Putative multidrug export ATP‑binding/permease protein |
| RA | USA300TCH1516_ALE | 2,150,242 | C→G | 6.3% | H208D (CAT→GAT) | agrA → | Accessory gene regulator A |
| RA | USA300TCH1516_ALE | 2,279,705 | G→A | 100% | A943V (GCA→GTA) | ebh_3 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 2,305,823 | C→T | 12.3% | intergenic (‑126/‑51) | ydjM ← / → USA300HOU_RS11765 | Inner membrane protein YdjM/hypothetical protein |
| RA | USA300TCH1516_ALE | 2,373,506 | A→T | 15.7% | N90K (AAT→AAA) | pbuG ← | Guanine/hypoxanthine permease PbuG |
| RA | USA300TCH1516_ALE | 2,504,989 | T→C | 9.0% | 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 | 2,771,843 | C→A | 8.3% | F214L (TTC→TTA) | phoB → | Alkaline phosphatase 3 |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | 37094 = | 98 (1.270) | 9 (0.130) | 4/240 | NT | 10.2% | intergenic (+118/‑719) | USA300HOU_RS14915/ugpQ_1 | hypothetical protein/Glycerophosphodiester phosphodiesterase, cytoplasmic |
| ? | USA300TCH1516_ALE | 37188 = | 68 (0.950) | intergenic (+212/‑625) | USA300HOU_RS14915/ugpQ_1 | hypothetical protein/Glycerophosphodiester phosphodiesterase, cytoplasmic | |||||
| * | ? | USA300TCH1516_ALE | 512620 = | 80 (1.030) | 68 (1.270) +40 bp |
44/180 | NT | 55.2% | 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 | 1822717 = | 59 (0.760) | 3 (0.040) | 3/238 | NT | 5.6% | intergenic (+38/+208) | USA300HOU_RS09070/ackA | Putative universal stress protein/Acetate kinase |
| ? | USA300TCH1516_ALE | 1822745 = | 48 (0.680) | intergenic (+66/+180) | USA300HOU_RS09070/ackA | Putative universal stress protein/Acetate kinase | |||||
| * | ? | USA300TCH1516_ALE | 2085296 = | 54 (0.700) | 13 (0.190) | 12/232 | NT | 18.6% | coding (173/201 nt) | hlb_1 | Phospholipase C |
| ? | USA300TCH1516_ALE | = 2128343 | 66 (0.960) | coding (1/825 nt) | hlb_2 | Phospholipase C | |||||