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 |
| RA | CP000731 | 6,310 | A→T | 6.6% | intergenic (+827/‑661) | cadX → / → USA300HOU_pUSA300HOUMR0010 | cadmium efflux regulator/MarR family transcriptional regulator |
| JC | CP000731 | 6,552 | +28 bp | 100% | intergenic (+1069/‑419) | cadX → / → USA300HOU_pUSA300HOUMR0010 | cadmium efflux regulator/MarR family transcriptional regulator |
| RA | CP000731 | 25,189 | C→A | 5.3% | intergenic (+87/‑159) | USA300HOU_pUSA300HOUMR0030 → / → USA300HOU_pUSA300HOUMR0031 | Sin recombinase/hypothetical protein |
| RA | CP000731 | 25,663 | Δ1 bp | 100% | coding (316/333 nt) | USA300HOU_pUSA300HOUMR0031 → | hypothetical protein |
| JC | USA300TCH1516_ALE | 68,656 | Δ3 bp | 5.4% | coding (772‑774/852 nt) | USA300TCH1516_00061 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 75,007 | C→T | 7.9% | M1M (ATG→ATA) † | argR_1 ← | Arginine repressor |
| RA | USA300TCH1516_ALE | 110,651 | C→T | 12.8% | D170D (GAC→GAT) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 110,660 | T→A | 17.0% | I173I (ATT→ATA) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,512 | A→G | 24.6% | S194S (TCA→TCG) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,516 | C→A | 24.3% | Q196K (CAA→AAA) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 235,092 | C→T | 6.5% | D490N (GAT→AAT) | gsiA ← | Glutathione import ATP‑binding protein GsiA |
| RA | USA300TCH1516_ALE | 293,940 | C→T | 19.6% | intergenic (+57/‑471) | gatD → / → tarI' | Galactitol‑1‑phosphate 5‑dehydrogenase/Ribitol‑5‑phosphate cytidylyltransferase 2 |
| RA | USA300TCH1516_ALE | 317,291 | A→G | 5.3% | M192T (ATG→ACG) | degA ← | HTH‑type transcriptional regulator DegA |
| RA | USA300TCH1516_ALE | 478,502 | C→A | 100% | D342E (GAC→GAA) | nuoL → | NADH‑quinone oxidoreductase subunit L |
| RA | USA300TCH1516_ALE | 512,643 | A→G | 45.8% | intergenic (+711/‑6052) | recR → / → speA_2 | Recombination protein RecR/Arginine decarboxylase |
| RA | USA300TCH1516_ALE | 584,121 | G→T | 100% | intergenic (+205/‑67) | rplA → / → rplJ | 50S ribosomal protein L1/50S ribosomal protein L10 |
| RA | USA300TCH1516_ALE | 622,479 | T→C | 10.0% | D1014D (GAT→GAC) | sdrE → | Serine‑aspartate repeat‑containing protein E |
| RA | USA300TCH1516_ALE | 628,618 | T→A | 6.9% | S8T (TCG→ACG) | nagB_1 → | Glucosamine‑6‑phosphate deaminase |
| RA | USA300TCH1516_ALE | 677,733 | A→G | 5.2% | I204V (ATT→GTT) | USA300HOU_RS03265 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 685,779 | T→C | 8.7% | L127L (TTA→TTG) | USA300HOU_RS03310 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 707,909 | A→T | 100% | M1M (TTG→ATG) † | znuC_1 ← | High‑affinity zinc uptake system ATP‑binding protein ZnuC |
| RA | USA300TCH1516_ALE | 973,213 | C→A | 100% | E175* (GAG→TAG) | yitU_1 ← | 5‑amino‑6‑(5‑phospho‑D‑ribitylamino)uracil phosphatase YitU |
| RA | USA300TCH1516_ALE | 1,002,200 | T→G | 100% | M173R (ATG→AGG) | mecA → | Adapter protein MecA 1 |
| RA | USA300TCH1516_ALE | 1,105,994 | T→C | 100% | T12T (ACT→ACC) | pdhD → | Dihydrolipoyl dehydrogenase |
| RA | USA300TCH1516_ALE | 1,133,417 | T→A | 5.7% | V146V (GTT→GTA) | rsmD → | Ribosomal RNA small subunit methyltransferase D |
| RA | USA300TCH1516_ALE | 1,134,851 | A→T | 5.4% | I119I (ATT→ATA) | USA300HOU_RS05620 ← | Nicotinamide‑nucleotide adenylyltransferase |
| RA | USA300TCH1516_ALE | 1,196,508 | C→A | 100% | S338Y (TCT→TAT) | ftsZ → | Cell division protein FtsZ |
| RA | USA300TCH1516_ALE | 1,249,530 | G→A | 5.7% | A956T (GCG→ACG) | smc_2 → | Chromosome partition protein Smc |
| 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 | 1,539,250 | C→G | 100% | intergenic (‑349/+37) | aroC ← / ← USA300HOU_RS07505 | Chorismate synthase/hypothetical protein |
| RA | USA300TCH1516_ALE | 1,617,132 | C→T | 5.6% | L212L (CTC→CTT) | yhdN_2 → | General stress protein 69 |
| RA | USA300TCH1516_ALE | 1,620,134 | C→T | 8.1% | A163A (GCG→GCA) | rnz ← | Ribonuclease Z |
| RA | USA300TCH1516_ALE | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | ypdF ← | Aminopeptidase YpdF |
| RA | USA300TCH1516_ALE | 1,744,473 | C→T | 100% | A67T (GCT→ACT) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,830,450 | T→C | 7.2% | T224A (ACT→GCT) | ezrA ← | Septation ring formation regulator EzrA |
| RA | USA300TCH1516_ALE | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | USA300HOU_RS10125 ← | Putative multidrug export ATP‑binding/permease protein |
| RA | USA300TCH1516_ALE | 2,184,114 | A→G | 5.3% | R277R (CGT→CGC) | rpsA_2 ← | 30S ribosomal protein S1 |
| RA | USA300TCH1516_ALE | 2,274,436 | A→G | 5.0% | T454T (ACA→ACG) | mtlA → | PTS system mannitol‑specific EIICB component |
| RA | USA300TCH1516_ALE | 2,279,705 | G→A | 100% | A943V (GCA→GTA) | ebh_3 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 2,337,959 | C→T | 100% | intergenic (‑125/‑283) | adhR ← / → USA300HOU_RS11940 | HTH‑type transcriptional regulator AdhR/Hyaluronate lyase |
| RA | USA300TCH1516_ALE | 2,343,438 | C→T | 33.3% | intergenic (+114/+250) | USA300HOU_RS11955 → / ← aldC_1 | 65 kDa membrane protein/Alpha‑acetolactate decarboxylase |
| RA | USA300TCH1516_ALE | 2,455,692 | Δ1 bp | 100% | coding (1210/1260 nt) | lyrA → | Lysostaphin resistance protein A |
| RA | USA300TCH1516_ALE | 2,455,698 | 2 bp→AT | 100% | coding (1216‑1217/1260 nt) | lyrA → | Lysostaphin resistance protein A |
| RA | USA300TCH1516_ALE | 2,468,887 | A→T | 5.6% | intergenic (‑76/‑132) | lipY ← / → USA300HOU_RS12715 | Triacylglycerol lipase/hypothetical protein |
| RA | USA300TCH1516_ALE | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
| RA | USA300TCH1516_ALE | 2,771,347 | C→A | 5.9% | P49Q (CCA→CAA) | phoB → | Alkaline phosphatase 3 |
| RA | USA300TCH1516_ALE | 2,774,969 | A→G | 6.8% | D739D (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 | 512620 = | 102 (1.350) | 57 (1.090) +40 bp |
32/180 | NT | 44.8% | 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 = | 50 (0.660) | 10 (0.150) | 8/226 | NT | 18.3% | coding (806/822 nt) | metQ_2 | Methionine‑binding lipoprotein MetQ |
| ? | USA300TCH1516_ALE | = 909740 | 46 (0.700) | intergenic (‑663/‑371) | USA300HOU_RS04500/csbD_1 | hypothetical protein/Stress response protein CsbD | |||||
| * | ? | USA300TCH1516_ALE | 2085296 = | 49 (0.650) | 19 (0.280) | 14/232 | NT | 26.1% | coding (173/201 nt) | hlb_1 | Phospholipase C |
| ? | USA300TCH1516_ALE | = 2128343 | 64 (0.950) | coding (1/825 nt) | hlb_2 | Phospholipase C | |||||
| * | ? | USA300TCH1516_ALE | = 2419897 | 90 (1.190) | 5 (0.080) | 4/228 | NT | 5.5% | intergenic (+65/‑172) | USA300HOU_RS12460/ssaA2_3 | hypothetical protein/Staphylococcal secretory antigen ssaA2 |
| ? | USA300TCH1516_ALE | = 2419903 | 92 (1.390) | intergenic (+71/‑166) | USA300HOU_RS12460/ssaA2_3 | hypothetical protein/Staphylococcal secretory antigen ssaA2 | |||||