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 |
| MC | CP000731 | 1 | Δ27,041 bp | 100% | repA–USA300HOU_pUSA300HOUMR0033 | 26 genes repA, USA300HOU_pUSA300HOUMR0003, USA300HOU_pUSA300HOUMR0004, USA300HOU_pUSA300HOUMR0005, USA300HOU_pUSA300HOUMR0006, cadR, cadX, USA300HOU_pUSA300HOUMR0010, blaZ, blaR, blaI, USA300HOU_pUSA300HOUMR0014, USA300HOU_pUSA300HOUMR0015, USA300HOU_pUSA300HOUMR0016, USA300HOU_pUSA300HOUMR0018, USA300HOU_pUSA300HOUMR0019, USA300HOU_pUSA300HOUMR0021, USA300HOU_pUSA300HOUMR0023, USA300HOU_pUSA300HOUMR0024, USA300HOU_pUSA300HOUMR0027, USA300HOU_pUSA300HOUMR0028, USA300HOU_pUSA300HOUMR0029, USA300HOU_pUSA300HOUMR0030, USA300HOU_pUSA300HOUMR0031, USA300HOU_pUSA300HOUMR0032, USA300HOU_pUSA300HOUMR0033 |
|
| RA | USA300TCH1516_ALE | 19,264 | G→A | 28.0% | G307D (GGC→GAC) | gdpP → | Cyclic‑di‑AMP phosphodiesterase GdpP |
| RA | USA300TCH1516_ALE | 19,294 | C→T | 48.6% | T317I (ACT→ATT) | gdpP → | Cyclic‑di‑AMP phosphodiesterase GdpP |
| RA | USA300TCH1516_ALE | 37,539 | C→A | 22.8% | intergenic (+563/‑274) | USA300HOU_RS14915 → / → ugpQ_1 | hypothetical protein/Glycerophosphodiester phosphodiesterase, cytoplasmic |
| RA | USA300TCH1516_ALE | 37,540 | A→G | 18.9% | intergenic (+564/‑273) | USA300HOU_RS14915 → / → ugpQ_1 | hypothetical protein/Glycerophosphodiester phosphodiesterase, cytoplasmic |
| RA | USA300TCH1516_ALE | 37,542 | T→C | 20.2% | intergenic (+566/‑271) | USA300HOU_RS14915 → / → ugpQ_1 | hypothetical protein/Glycerophosphodiester phosphodiesterase, cytoplasmic |
| RA | USA300TCH1516_ALE | 37,551 | T→A | 39.8% | intergenic (+575/‑262) | USA300HOU_RS14915 → / → ugpQ_1 | hypothetical protein/Glycerophosphodiester phosphodiesterase, cytoplasmic |
| RA | USA300TCH1516_ALE | 37,558 | G→A | 51.4% | intergenic (+582/‑255) | USA300HOU_RS14915 → / → ugpQ_1 | hypothetical protein/Glycerophosphodiester phosphodiesterase, cytoplasmic |
| RA | USA300TCH1516_ALE | 37,562 | A→G | 58.2% | intergenic (+586/‑251) | USA300HOU_RS14915 → / → ugpQ_1 | hypothetical protein/Glycerophosphodiester phosphodiesterase, cytoplasmic |
| RA | USA300TCH1516_ALE | 37,563 | A→C | 58.1% | intergenic (+587/‑250) | USA300HOU_RS14915 → / → ugpQ_1 | hypothetical protein/Glycerophosphodiester phosphodiesterase, cytoplasmic |
| RA | USA300TCH1516_ALE | 37,574 | A→G | 62.7% | intergenic (+598/‑239) | USA300HOU_RS14915 → / → ugpQ_1 | hypothetical protein/Glycerophosphodiester phosphodiesterase, cytoplasmic |
| RA | USA300TCH1516_ALE | 37,576 | C→T | 63.5% | intergenic (+600/‑237) | USA300HOU_RS14915 → / → ugpQ_1 | hypothetical protein/Glycerophosphodiester phosphodiesterase, cytoplasmic |
| RA | USA300TCH1516_ALE | 37,579 | A→C | 61.2% | intergenic (+603/‑234) | USA300HOU_RS14915 → / → ugpQ_1 | hypothetical protein/Glycerophosphodiester phosphodiesterase, cytoplasmic |
| RA | USA300TCH1516_ALE | 37,591 | A→T | 61.9% | intergenic (+615/‑222) | USA300HOU_RS14915 → / → ugpQ_1 | hypothetical protein/Glycerophosphodiester phosphodiesterase, cytoplasmic |
| RA | USA300TCH1516_ALE | 39,378 | C→T | 75.3% | D586N (GAT→AAT) | pbp ← | Beta‑lactam‑inducible penicillin‑binding protein |
| RA | USA300TCH1516_ALE | 39,672 | C→A | 29.3% | V488F (GTT→TTT) | pbp ← | Beta‑lactam‑inducible penicillin‑binding protein |
| RA | USA300TCH1516_ALE | 76,969 | G→A | 31.5% | intergenic (+509/‑107) | USA300HOU_RS00140 → / → USA300HOU_RS00350 | hypothetical protein/Monoacylglycerol lipase |
| RA | USA300TCH1516_ALE | 110,651 | C→T | 6.0% | D170D (GAC→GAT) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 110,660 | T→A | 8.5% | I173I (ATT→ATA) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,512 | A→G | 28.3% | S194S (TCA→TCG) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,516 | C→A | 27.2% | Q196K (CAA→AAA) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,560 | T→C | 6.4% | R210R (CGT→CGC) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 195,286 | T→A | 22.1% | intergenic (‑97/‑82) | USA300HOU_RS00900 ← / → USA300HOU_RS00905 | hypothetical protein/hypothetical protein |
| RA | USA300TCH1516_ALE | 396,540 | G→A | 25.9% | A208T (GCA→ACA) | efeM → | putative iron uptake system component EfeM |
| RA | USA300TCH1516_ALE | 478,502 | C→A | 71.0% | D342E (GAC→GAA) | nuoL → | NADH‑quinone oxidoreductase subunit L |
| RA | USA300TCH1516_ALE | 512,643 | A→G | 58.4% | intergenic (+711/‑6052) | recR → / → speA_2 | Recombination protein RecR/Arginine decarboxylase |
| RA | USA300TCH1516_ALE | 584,121 | G→T | 77.7% | intergenic (+205/‑67) | rplA → / → rplJ | 50S ribosomal protein L1/50S ribosomal protein L10 |
| RA | USA300TCH1516_ALE | 607,884 | G→A | 30.7% | R209* (CGA→TGA) | dck ← | Deoxyadenosine/deoxycytidine kinase |
| RA | USA300TCH1516_ALE | 629,681 | C→A | 27.2% | L84I (CTA→ATA) | USA300HOU_RS02990 → | 3‑hexulose‑6‑phosphate synthase |
| RA | USA300TCH1516_ALE | 665,392 | T→G | 19.9% | L79* (TTA→TGA) | paiA_1 → | Spermidine/spermine N(1)‑acetyltransferase |
| RA | USA300TCH1516_ALE | 694,071 | G→T | 13.7% | A50E (GCA→GAA) | USA300HOU_RS03355 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 707,909 | A→T | 69.3% | M1M (TTG→ATG) † | znuC_1 ← | High‑affinity zinc uptake system ATP‑binding protein ZnuC |
| RA | USA300TCH1516_ALE | 707,910 | A→G | 31.5% | intergenic (‑1/‑121) | znuC_1 ← / → ideR | High‑affinity zinc uptake system ATP‑binding protein ZnuC/Iron‑dependent repressor IdeR |
| RA | USA300TCH1516_ALE | 804,673 | A→T | 27.0% | L135I (TTA→ATA) | dtpT ← | Di‑/tripeptide transporter |
| RA | USA300TCH1516_ALE | 828,298 | T→A | 7.5% | intergenic (+213/‑151) | USA300HOU_RS04050 → / → comFA | DegV domain‑containing protein/ComF operon protein 1 |
| RA | USA300TCH1516_ALE | 864,745 | C→G | 6.6% | L21V (CTA→GTA) | est_2 → | Carboxylesterase |
| RA | USA300TCH1516_ALE | 973,213 | C→A | 72.2% | E175* (GAG→TAG) | yitU_1 ← | 5‑amino‑6‑(5‑phospho‑D‑ribitylamino)uracil phosphatase YitU |
| RA | USA300TCH1516_ALE | 1,002,200 | T→G | 77.7% | M173R (ATG→AGG) | mecA → | Adapter protein MecA 1 |
| RA | USA300TCH1516_ALE | 1,064,444 | Δ1 bp | 27.9% | coding (45/1218 nt) | ywtF ← | Putative transcriptional regulator YwtF |
| RA | USA300TCH1516_ALE | 1,105,994 | T→C | 69.2% | T12T (ACT→ACC) | pdhD → | Dihydrolipoyl dehydrogenase |
| RA | USA300TCH1516_ALE | 1,151,773 | T→C | 5.2% | I7T (ATC→ACC) | polX → | DNA polymerase/3'‑5' exonuclease PolX |
| RA | USA300TCH1516_ALE | 1,196,508 | C→A | 62.7% | S338Y (TCT→TAT) | ftsZ → | Cell division protein FtsZ |
| RA | USA300TCH1516_ALE | 1,231,470 | A→C | 6.4% | M39L (ATG→CTG) | stp → | Serine/threonine phosphatase stp |
| RA | USA300TCH1516_ALE | 1,232,148 | G→C | 68.1% | G18A (GGC→GCC) | prkC → | Serine/threonine‑protein kinase PrkC |
| RA | USA300TCH1516_ALE | 1,233,504 | T→A | 31.2% | V470D (GTT→GAT) | prkC → | Serine/threonine‑protein kinase PrkC |
| RA | USA300TCH1516_ALE | 1,415,237 | T→A | 5.1% | I92L (ATA→TTA) | mqo ← | malate:quinone oxidoreductase |
| RA | USA300TCH1516_ALE | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | oppD_4 ← | Oligopeptide transport ATP‑binding protein OppD |
| RA | USA300TCH1516_ALE | 1,440,085 | G→T | 38.7% | intergenic (‑45/+126) | cspA_2 ← / ← USA300TCH1516_01338 | Cold shock protein CspA/hypothetical protein |
| RA | USA300TCH1516_ALE | 1,513,930 | A→T | 100% | L413F (TTA→TTT) | USA300HOU_RS07375 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,539,250 | C→G | 64.8% | intergenic (‑349/+37) | aroC ← / ← USA300HOU_RS07505 | Chorismate synthase/hypothetical protein |
| RA | USA300TCH1516_ALE | 1,551,935 | G→T | 5.7% | S180* (TCA→TAA) | ebpS ← | Elastin‑binding protein EbpS |
| RA | USA300TCH1516_ALE | 1,577,317 | A→T | 9.4% | V67D (GTT→GAT) | USA300HOU_RS07705 ← | Glycyl‑glycine endopeptidase ALE‑1 |
| RA | USA300TCH1516_ALE | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | ypdF ← | Aminopeptidase YpdF |
| RA | USA300TCH1516_ALE | 1,744,362 | G→A | 20.9% | H104Y (CAC→TAC) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,744,473 | C→T | 71.6% | A67T (GCT→ACT) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,749,331 | C→A | 36.0% | G40C (GGT→TGT) | USA300HOU_RS08710 ← | Heme uptake protein MmpL11 |
| RA | USA300TCH1516_ALE | 1,761,889 | C→A | 17.4% | D388Y (GAT→TAT) | fpgS ← | Folylpolyglutamate synthase |
| RA | USA300TCH1516_ALE | 1,776,265 | C→A | 11.1% | V87L (GTA→TTA) | clpX ← | ATP‑dependent Clp protease ATP‑binding subunit ClpX |
| RA | USA300TCH1516_ALE | 1,808,702 | A→T | 6.8% | I204I (ATT→ATA) | accA ← | Acetyl‑coenzyme A carboxylase carboxyl transferase subunit alpha |
| RA | USA300TCH1516_ALE | 1,912,184 | T→G | 32.7% | N167K (AAT→AAG) | USA300HOU_RS15290 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,963,768 | C→G | 24.0% | V365L (GTA→CTA) | hemY ← | Protoporphyrinogen oxidase |
| RA | USA300TCH1516_ALE | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | USA300HOU_RS10125 ← | Putative multidrug export ATP‑binding/permease protein |
| RA | USA300TCH1516_ALE | 2,028,394 | A→C | 68.3% | F84C (TTT→TGT) | USA300HOU_RS10230 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,028,583 | G→T | 25.2% | A21D (GCC→GAC) | USA300HOU_RS10230 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,123,847 | T→A | 7.8% | intergenic (‑107/‑26) | USA300HOU_RS10825 ← / → lexA_2 | hypothetical protein/LexA repressor |
| 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 | 71.7% | intergenic (‑125/‑283) | adhR ← / → USA300HOU_RS11940 | HTH‑type transcriptional regulator AdhR/Hyaluronate lyase |
| RA | USA300TCH1516_ALE | 2,352,815 | G→A | 27.9% | A92V (GCA→GTA) | rpsI ← | 30S ribosomal protein S9 |
| RA | USA300TCH1516_ALE | 2,454,626 | A→T | 30.2% | L48L (CTA→CTT) | lyrA → | Lysostaphin resistance protein A |
| RA | USA300TCH1516_ALE | 2,455,692 | Δ1 bp | 59.1% | coding (1210/1260 nt) | lyrA → | Lysostaphin resistance protein A |
| RA | USA300TCH1516_ALE | 2,455,699 | A→T | 68.2% | H406L (CAT→CTT) | lyrA → | Lysostaphin resistance protein A |
| RA | USA300TCH1516_ALE | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
| RA | USA300TCH1516_ALE | 2,542,325 | G→T | 69.2% | A29S (GCC→TCC) | hlgA → | Gamma‑hemolysin component A |
| RA | USA300TCH1516_ALE | 2,562,956 | A→C | 7.2% | I211L (ATT→CTT) | cycA_2 → | D‑serine/D‑alanine/glycine transporter |
| RA | USA300TCH1516_ALE | 2,774,846 | A→G | 13.0% | S780S (AGT→AGC) | clfB ← | Clumping factor B |
| RA | USA300TCH1516_ALE | 2,799,069 | G→T | 9.2% | Q516K (CAA→AAA) | USA300HOU_RS14380 ← | hypothetical protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | 512620 = | 83 (0.810) | 86 (1.220) +40 bp |
59/180 | NT | 60.0% | 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 | = 800928 | 92 (0.900) | 9 (0.090) | 8/246 | NT | 8.2% | intergenic (+62/‑289) | hisC_1/USA300HOU_RS03915 | Histidinol‑phosphate aminotransferase/Putative 5'(3')‑deoxyribonucleotidase |
| ? | USA300TCH1516_ALE | 801948 = | 115 (1.190) | intergenic (+189/+435) | USA300HOU_RS03915/USA300HOU_RS03920 | Putative 5'(3')‑deoxyribonucleotidase/Putative lipid kinase | |||||
| * | ? | USA300TCH1516_ALE | 2257232 = | 80 (0.780) | 4 (0.040) | 3/248 | NT | 5.2% | coding (293/414 nt) | USA300HOU_RS11555 | hypothetical protein |
| ? | USA300TCH1516_ALE | 2257282 = | 71 (0.730) | coding (243/414 nt) | USA300HOU_RS11555 | hypothetical protein | |||||