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 | annotation | gene | description |
RA | CP000731 | 81 | N→G | intergenic (–/‑151) | – / → repA | –/replication protein A |
JC | CP000731 | 6,552 | +28 bp | intergenic (+1069/‑419) | cadX → / → USA300HOU_pUSA300HOUMR0010 | cadmium efflux regulator/MarR family transcriptional regulator |
RA | CP000731 | 25,669 | (A)7→6 | coding (322/333 nt) | USA300HOU_pUSA300HOUMR0031 → | hypothetical protein |
RA | USA300TCH1516_ALE | 127,420 | G→T | L411F (TTG→TTT) | lctP_1 → | L‑lactate permease |
RA | USA300TCH1516_ALE | 733,536 | G→T | S207I (AGT→ATT) | graR_1 → | Response regulator protein GraR |
RA | USA300TCH1516_ALE | 1,054,623 | G→A | intergenic (‑124/+404) | sspA ← / ← patA_2 | Glutamyl endopeptidase/Putative N‑acetyl‑LL‑diaminopimelate aminotransferase |
RA | USA300TCH1516_ALE | 1,416,458 | A→T | I216N (ATT→AAT) | oppD_4 ← | Oligopeptide transport ATP‑binding protein OppD |
RA | USA300TCH1516_ALE | 1,513,930 | A→T | L413F (TTA→TTT) | USA300HOU_RS07375 → | hypothetical protein |
RA | USA300TCH1516_ALE | 1,646,189 | G→C | A155G (GCA→GGA) | ypdF ← | Aminopeptidase YpdF |
RA | USA300TCH1516_ALE | 2,010,363 | C→T | C146Y (TGT→TAT) | USA300HOU_RS10125 ← | Putative multidrug export ATP‑binding/permease protein |
RA | USA300TCH1516_ALE | 2,018,582 | T→A | K113* (AAA→TAA) | mgt ← | Monofunctional glycosyltransferase |
RA | USA300TCH1516_ALE | 2,279,705 | G→A | A943V (GCA→GTA) | ebh_3 ← | Extracellular matrix‑binding protein ebh |
RA | USA300TCH1516_ALE | 2,373,531 | G→T | A82E (GCG→GAG) | pbuG ← | Guanine/hypoxanthine permease PbuG |
RA | USA300TCH1516_ALE | 2,532,298 | A→T | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
Unassigned missing coverage evidence | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
seq id | start | end | size | ←reads | reads→ | gene | description | |||
* | * | ÷ | USA300TCH1516_ALE | 2176699–2181157 | 2181157 | 1–4459 | 3 [2] | [2] 3 | ilvA/USA300TCH1516_02069 | L‑threonine dehydratase biosynthetic IlvA/tRNA‑Gly |
Unassigned new junction evidence | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | USA300TCH1516_ALE | 895785 = | 28 (1.520) | 12 (0.750) | 10/234 | 0.5 | 35.6% | coding (806/822 nt) | metQ_2 | Methionine‑binding lipoprotein MetQ |
? | USA300TCH1516_ALE | = 909740 | 19 (1.180) | intergenic (‑663/‑371) | USA300HOU_RS04500/csbD_1 | hypothetical protein/Stress response protein CsbD | |||||
* | ? | USA300TCH1516_ALE | 2085296 = | 15 (0.810) | 9 (0.550) | 9/240 | 0.7 | 37.2% | coding (173/201 nt) | hlb_1 | Phospholipase C |
? | USA300TCH1516_ALE | = 2128343 | 17 (1.030) | coding (1/825 nt) | hlb_2 | Phospholipase C |