mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | USA300TCH1516_ALE | 110,651 | C→T | 8.3% | D170D (GAC→GAT) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 110,660 | T→A | 13.8% | I173I (ATT→ATA) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,512 | A→G | 31.1% | S194S (TCA→TCG) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,516 | C→A | 30.1% | Q196K (CAA→AAA) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,560 | T→C | 7.0% | R210R (CGT→CGC) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 128,994 | C→T | 6.0% | L198L (TTG→TTA) | spa ← | Immunoglobulin G‑binding protein A |
| RA | USA300TCH1516_ALE | 151,520 | C→A | 5.3% | S117R (AGC→AGA) | USA300HOU_RS00690 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 456,608 | A→T | 6.7% | E55D (GAA→GAT) | tst_4 → | Toxic shock syndrome toxin‑1 |
| RA | USA300TCH1516_ALE | 486,180 | G→T | 5.3% | intergenic (+56/‑161) | USA300TCH1516_00437 → / → mccA | hypothetical protein/O‑acetylserine dependent cystathionine beta‑synthase |
| RA | USA300TCH1516_ALE | 512,643 | A→G | 47.0% | intergenic (+711/‑6052) | recR → / → speA_2 | Recombination protein RecR/Arginine decarboxylase |
| JC | USA300TCH1516_ALE | 514,457 | Δ16 bp | 60.4% | intergenic (+2525/‑4223) | recR → / → speA_2 | Recombination protein RecR/Arginine decarboxylase |
| RA | USA300TCH1516_ALE | 614,094 | T→C | 5.5% | S802S (AGT→AGC) | sdrC → | Serine‑aspartate repeat‑containing protein C |
| RA | USA300TCH1516_ALE | 614,172 | T→C | 5.1% | S828S (AGT→AGC) | sdrC → | Serine‑aspartate repeat‑containing protein C |
| RA | USA300TCH1516_ALE | 618,351 | T→C | 7.7% | D1151D (GAT→GAC) | sdrD → | Serine‑aspartate repeat‑containing protein D |
| RA | USA300TCH1516_ALE | 618,387 | T→C | 6.0% | D1163D (GAT→GAC) | sdrD → | Serine‑aspartate repeat‑containing protein D |
| RA | USA300TCH1516_ALE | 618,489 | T→C | 7.3% | D1197D (GAT→GAC) | sdrD → | Serine‑aspartate repeat‑containing protein D |
| RA | USA300TCH1516_ALE | 618,513 | T→C | 5.4% | D1205D (GAT→GAC) | sdrD → | Serine‑aspartate repeat‑containing protein D |
| RA | USA300TCH1516_ALE | 618,567 | T→C | 5.3% | D1223D (GAT→GAC) | sdrD → | Serine‑aspartate repeat‑containing protein D |
| RA | USA300TCH1516_ALE | 618,621 | T→C | 5.1% | D1241D (GAT→GAC) | sdrD → | Serine‑aspartate repeat‑containing protein D |
| RA | USA300TCH1516_ALE | 618,636 | G→A | 6.8% | S1246S (TCG→TCA) | sdrD → | Serine‑aspartate repeat‑containing protein D |
| RA | USA300TCH1516_ALE | 618,657 | T→C | 6.9% | D1253D (GAT→GAC) | sdrD → | Serine‑aspartate repeat‑containing protein D |
| RA | USA300TCH1516_ALE | 618,666 | T→C | 5.3% | S1256S (AGT→AGC) | sdrD → | Serine‑aspartate repeat‑containing protein D |
| RA | USA300TCH1516_ALE | 618,693 | T→C | 6.8% | D1265D (GAT→GAC) | sdrD → | Serine‑aspartate repeat‑containing protein D |
| RA | USA300TCH1516_ALE | 618,714 | G→A | 6.4% | S1272S (TCG→TCA) | sdrD → | Serine‑aspartate repeat‑containing protein D |
| RA | USA300TCH1516_ALE | 622,359 | T→C | 6.8% | D974D (GAT→GAC) | sdrE → | Serine‑aspartate repeat‑containing protein E |
| RA | USA300TCH1516_ALE | 622,464 | G→A | 9.5% | S1009S (TCG→TCA) | sdrE → | Serine‑aspartate repeat‑containing protein E |
| RA | USA300TCH1516_ALE | 622,479 | T→C | 5.1% | D1014D (GAT→GAC) | sdrE → | Serine‑aspartate repeat‑containing protein E |
| RA | USA300TCH1516_ALE | 622,521 | T→C | 5.8% | D1028D (GAT→GAC) | sdrE → | Serine‑aspartate repeat‑containing protein E |
| RA | USA300TCH1516_ALE | 622,533 | T→C | 6.0% | D1032D (GAT→GAC) | sdrE → | Serine‑aspartate repeat‑containing protein E |
| RA | USA300TCH1516_ALE | 622,536 | G→A | 6.7% | S1033S (TCG→TCA) | sdrE → | Serine‑aspartate repeat‑containing protein E |
| RA | USA300TCH1516_ALE | 776,295 | G→T | 5.2% | intergenic (+97/‑124) | nagA → / → corC | N‑acetylglucosamine‑6‑phosphate deacetylase/Magnesium and cobalt efflux protein CorC |
| RA | USA300TCH1516_ALE | 1,141,234 | T→A | 6.6% | S285T (TCA→ACA) | USA300HOU_RS05655 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,333,789 | T→G | 6.6% | Y64D (TAT→GAT) | hflX → | GTPase HflX |
| RA | USA300TCH1516_ALE | 1,370,154 | C→A | 5.4% | A15D (GCT→GAT) | USA300TCH1516_01280 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | oppD_4 ← | Oligopeptide transport ATP‑binding protein OppD |
| RA | USA300TCH1516_ALE | 1,435,065 | C→G | 10.3% | A141G (GCT→GGT) | dapH → | 2,3,4,5‑tetrahydropyridine‑2,6‑dicarboxylate N‑acetyltransferase |
| RA | USA300TCH1516_ALE | 1,435,073 | G→A | 10.0% | G144S (GGT→AGT) ‡ | dapH → | 2,3,4,5‑tetrahydropyridine‑2,6‑dicarboxylate N‑acetyltransferase |
| RA | USA300TCH1516_ALE | 1,435,075 | T→A | 6.7% | G144G (GGT→GGA) ‡ | dapH → | 2,3,4,5‑tetrahydropyridine‑2,6‑dicarboxylate N‑acetyltransferase |
| RA | USA300TCH1516_ALE | 1,435,081 | T→A | 8.7% | N146K (AAT→AAA) | dapH → | 2,3,4,5‑tetrahydropyridine‑2,6‑dicarboxylate N‑acetyltransferase |
| RA | USA300TCH1516_ALE | 1,472,936 | A→T | 6.4% | A9696A (GCT→GCA) | ebh_1 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 1,473,069 | C→T | 5.4% | G9652D (GGC→GAC) | ebh_1 ← | Extracellular matrix‑binding protein ebh |
| 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 | 1,744,428 | T→C | 7.5% | K82E (AAA→GAA) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,857,785 | A→T | 12.2% | S197T (TCA→ACA) | USA300HOU_RS09235 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,857,867 | C→T | 12.0% | L169L (TTG→TTA) | USA300HOU_RS09235 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,857,944 | A→T | 8.6% | S144T (TCA→ACA) | 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 | 2,018,582 | T→A | 6.9% | K113* (AAA→TAA) | mgt ← | Monofunctional glycosyltransferase |
| RA | USA300TCH1516_ALE | 2,018,819 | G→T | 5.6% | P34T (CCG→ACG) | mgt ← | Monofunctional glycosyltransferase |
| RA | USA300TCH1516_ALE | 2,028,124 | G→A | 69.7% | P174L (CCG→CTG) | USA300HOU_RS10230 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,028,652 | C→T | 9.6% | intergenic (‑8/+7) | USA300HOU_RS10230 ← / ← USA300HOU_RS10235 | hypothetical protein/hypothetical protein |
| RA | USA300TCH1516_ALE | 2,124,510 | C→A | 7.3% | S213* (TCA→TAA) | lexA_2 → | LexA repressor |
| RA | USA300TCH1516_ALE | 2,124,529 | C→A | 8.0% | D219E (GAC→GAA) | lexA_2 → | LexA repressor |
| RA | USA300TCH1516_ALE | 2,211,305 | A→G | 5.5% | 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 | 2,281,993 | A→T | 7.4% | N180K (AAT→AAA) | ebh_3 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 2,358,670 | T→C | 6.7% | K83R (AAA→AGA) | rpoA_1 ← | DNA‑directed RNA polymerase subunit alpha |
| RA | USA300TCH1516_ALE | 2,372,751 | A→T | 68.8% | L342* (TTA→TAA) | pbuG ← | Guanine/hypoxanthine permease PbuG |
| RA | USA300TCH1516_ALE | 2,373,531 | G→T | 8.2% | A82E (GCG→GAG) | pbuG ← | Guanine/hypoxanthine permease PbuG |
| RA | USA300TCH1516_ALE | 2,373,714 | C→T | 5.7% | G21D (GGT→GAT) | pbuG ← | Guanine/hypoxanthine permease PbuG |
| RA | USA300TCH1516_ALE | 2,462,758 | G→A | 61.7% | A70T (GCA→ACA) | USA300HOU_RS12680 → | Putative 3‑methyladenine DNA glycosylase |
| RA | USA300TCH1516_ALE | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
| RA | USA300TCH1516_ALE | 2,774,816 | C→T | 6.8% | S790S (TCG→TCA) | clfB ← | Clumping factor B |
| RA | USA300TCH1516_ALE | 2,774,855 | A→G | 5.4% | D777D (GAT→GAC) | clfB ← | Clumping factor B |
| RA | USA300TCH1516_ALE | 2,774,930 | C→T | 6.4% | S752S (TCG→TCA) | clfB ← | Clumping factor B |
| RA | USA300TCH1516_ALE | 2,774,981 | A→G | 6.5% | D735D (GAT→GAC) | clfB ← | Clumping factor B |
| RA | USA300TCH1516_ALE | 2,775,041 | A→G | 5.6% | D715D (GAT→GAC) | clfB ← | Clumping factor B |
| RA | USA300TCH1516_ALE | 2,775,089 | A→G | 7.7% | D699D (GAT→GAC) | clfB ← | Clumping factor B |
| RA | USA300TCH1516_ALE | 2,775,287 | A→G | 5.7% | D633D (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 | 52495 = | 282 (0.770) | 342 (0.950) +T |
9/258 | NT | 53.3% | intergenic (+105/‑568) | USA300HOU_RS00215/USA300HOU_RS00220 | hypothetical protein/hypothetical protein |
| ? | USA300TCH1516_ALE | = 52988 | 321 (0.880) | intergenic (+598/‑75) | USA300HOU_RS00215/USA300HOU_RS00220 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 512620 = | 394 (1.080) | 278 (1.100) +40 bp |
108/180 | NT | 50.6% | 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 | 895785 = | 318 (0.870) | 29 (0.090) | 23/226 | NT | 9.5% | coding (806/822 nt) | metQ_2 | Methionine‑binding lipoprotein MetQ |
| ? | USA300TCH1516_ALE | = 909740 | 276 (0.870) | intergenic (‑663/‑371) | USA300HOU_RS04500/csbD_1 | hypothetical protein/Stress response protein CsbD | |||||
| * | ? | USA300TCH1516_ALE | 2085296 = | 302 (0.830) | 25 (0.080) | 20/232 | NT | 8.2% | coding (173/201 nt) | hlb_1 | Phospholipase C |
| ? | USA300TCH1516_ALE | = 2128343 | 294 (0.900) | coding (1/825 nt) | hlb_2 | Phospholipase C | |||||