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 USA300TCH1516_ALE 9,085 G→A R685H (CGT→CAT)  gyrA → DNA gyrase subunit A
RA USA300TCH1516_ALE 39,378 C→A D586Y (GAT→TAT)  pbp ← Beta‑lactam‑inducible penicillin‑binding protein
RA USA300TCH1516_ALE 76,969 G→A intergenic (+509/‑107) USA300HOU_RS00140 → / → USA300HOU_RS00350 hypothetical protein/Monoacylglycerol lipase
RA USA300TCH1516_ALE 195,286 T→A intergenic (‑97/‑82) USA300HOU_RS00900 ← / → USA300HOU_RS00905 hypothetical protein/hypothetical protein
RA USA300TCH1516_ALE 396,540 G→A A208T (GCA→ACA)  efeM → putative iron uptake system component EfeM
RA USA300TCH1516_ALE 607,884 G→A R209* (CGA→TGA)  dck ← Deoxyadenosine/deoxycytidine kinase
RA USA300TCH1516_ALE 629,681 C→A L84I (CTA→ATA)  USA300HOU_RS02990 → 3‑hexulose‑6‑phosphate synthase
RA USA300TCH1516_ALE 665,392 T→G L79* (TTA→TGA)  paiA_1 → Spermidine/spermine N(1)‑acetyltransferase
RA USA300TCH1516_ALE 1,274,208 C→T S204L (TCA→TTA)  codY → GTP‑sensing transcriptional pleiotropic repressor CodY
RA USA300TCH1516_ALE 1,416,458 A→T I216N (ATT→AAT)  oppD_4 ← Oligopeptide transport ATP‑binding protein OppD
RA USA300TCH1516_ALE 1,440,085 G→T intergenic (‑45/+126) cspA_2 ← / ← USA300TCH1516_01338 Cold shock protein CspA/hypothetical protein
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 1,744,362 G→A H104Y (CAC→TAC)  apt ← Adenine phosphoribosyltransferase
RA USA300TCH1516_ALE 1,761,889 C→A D388Y (GAT→TAT)  fpgS ← Folylpolyglutamate synthase
RA USA300TCH1516_ALE 1,909,490 +T coding (297/303 nt) USA300HOU_RS09460 → hypothetical protein
RA USA300TCH1516_ALE 1,963,768 C→G V365L (GTA→CTA)  hemY ← Protoporphyrinogen oxidase
RA USA300TCH1516_ALE 2,010,363 C→T C146Y (TGT→TAT)  USA300HOU_RS10125 ← Putative multidrug export ATP‑binding/permease protein
RA USA300TCH1516_ALE 2,028,269 G→C P126A (CCA→GCA)  USA300HOU_RS10230 ← hypothetical protein
RA USA300TCH1516_ALE 2,279,705 G→A A943V (GCA→GTA)  ebh_3 ← Extracellular matrix‑binding protein ebh
RA USA300TCH1516_ALE 2,352,815 G→A A92V (GCA→GTA)  rpsI ← 30S ribosomal protein S9
RA USA300TCH1516_ALE 2,405,489 G→T intergenic (‑136/‑124) USA300HOU_RS12375 ← / → ureA Urea transporter/Urease subunit gamma
RA USA300TCH1516_ALE 2,454,626 A→T L48L (CTA→CTT)  lyrA → Lysostaphin resistance protein A
RA USA300TCH1516_ALE 2,532,298 A→T T15T (ACA→ACT)  femA_3 → Aminoacyltransferase FemA
RA USA300TCH1516_ALE 2,679,725 G→A W70* (TGG→TAG)  ssaA2_4 → Staphylococcal secretory antigen ssaA2
JC USA300TCH1516_ALE 2,709,677 Δ12 bp coding (1239‑1250/1812 nt) oatA_2 ← O‑acetyltransferase OatA

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ CP000731 1 303 303 NA [0] [1] 2 [repA] [repA]
* * ÷ CP000731 423 601 179 2 [1] [1] 2 repA replication protein A
* * ÷ CP000731 1015 1141 127 2 [1] [1] 2 repA replication protein A
* * ÷ CP000731 1646 1880 235 2 [1] [1] 2 repA/USA300HOU_pUSA300HOUMR0003 replication protein A/hypothetical protein
* * ÷ CP000731 2251 2547 297 2 [1] [1] 2 [USA300HOU_pUSA300HOUMR0004] [USA300HOU_pUSA300HOUMR0004]
* * ÷ CP000731 2810 2899 90 2 [1] [1] 2 USA300HOU_pUSA300HOUMR0004 hypothetical protein
* * ÷ CP000731 3301 3391 91 2 [1] [1] 2 [USA300HOU_pUSA300HOUMR0005] [USA300HOU_pUSA300HOUMR0005]
* * ÷ CP000731 3719 3931 213 2 [1] [1] 2 [USA300HOU_pUSA300HOUMR0006] [USA300HOU_pUSA300HOUMR0006]
* * ÷ CP000731 4540 4813 274 2 [1] [1] 2 cadR cadmium binding protein
* * ÷ CP000731 5038 5324 287 2 [1] [1] 2 [cadR]–[cadX] [cadR],[cadX]
* * ÷ CP000731 5466 5510 45 2 [1] [1] 2 [cadX] [cadX]
* * ÷ CP000731 6431 6582 152 2 [1] [1] 2 cadX/USA300HOU_pUSA300HOUMR0010 cadmium efflux regulator/MarR family transcriptional regulator
* * ÷ CP000731 7077 7333 257 2 [1] [1] 3 USA300HOU_pUSA300HOUMR0010 MarR family transcriptional regulator
* * ÷ CP000731 8444 8708 265 2 [1] [1] 2 blaZ beta‑lactamase
* * ÷ CP000731 9484 9621 138 2 [1] [1] 2 blaR beta‑lactamase regulator BlaR
* * ÷ CP000731 10306 10473 168 2 [1] [1] 2 blaR beta‑lactamase regulator BlaR
* * ÷ CP000731 11175 11366 192 2 [1] [0] 2 [USA300HOU_pUSA300HOUMR0014] [USA300HOU_pUSA300HOUMR0014]
* * ÷ CP000731 11508 11922 415 3 [1] [1] 2 [USA300HOU_pUSA300HOUMR0014] [USA300HOU_pUSA300HOUMR0014]
* * ÷ CP000731 12064 12204 141 2 [1] [1] 2 USA300HOU_pUSA300HOUMR0015 hypothetical protein
* * ÷ CP000731 12346 12460 115 2 [1] [1] 2 USA300HOU_pUSA300HOUMR0015/USA300HOU_pUSA300HOUMR0016 hypothetical protein/IS257 transposase
* * ÷ CP000731 13376 13628 253 2 [1] [1] 2 USA300HOU_pUSA300HOUMR0016/USA300HOU_pUSA300HOUMR0018 IS257 transposase/3',5' aminoglycoside phosphotransferase
* * ÷ CP000731 13710 13866 157 2 [1] [1] 2 USA300HOU_pUSA300HOUMR0016/USA300HOU_pUSA300HOUMR0018 IS257 transposase/3',5' aminoglycoside phosphotransferase
* * ÷ CP000731 14773 14942 170 2 [1] [1] 2 USA300HOU_pUSA300HOUMR0018 3',5' aminoglycoside phosphotransferase
* * ÷ CP000731 15359 15591 233 2 [1] [1] 2 USA300HOU_pUSA300HOUMR0019 strepthothricin acetyltransferase
* * ÷ CP000731 16098 16114 17 2 [1] [1] 2 USA300HOU_pUSA300HOUMR0019/USA300HOU_pUSA300HOUMR0021 strepthothricin acetyltransferase/IS431 mec transposase
* * ÷ CP000731 16256 17675 1420 2 [1] [1] 2 USA300HOU_pUSA300HOUMR0021–[USA300HOU_pUSA300HOUMR0023] USA300HOU_pUSA300HOUMR0021,[USA300HOU_pUSA300HOUMR0023]
* * ÷ CP000731 18400 18857 458 2 [0] [1] 2 USA300HOU_pUSA300HOUMR0024 bacitracin ABC ATP binding cassette transporter, ABC protein
* * ÷ CP000731 18989 19244 256 2 [1] [1] 2 USA300HOU_pUSA300HOUMR0024/USA300HOU_pUSA300HOUMR0027 bacitracin ABC ATP binding cassette transporter, ABC protein/IS431mec transposase
* * ÷ CP000731 19557 19824 268 2 [1] [1] 2 USA300HOU_pUSA300HOUMR0024/USA300HOU_pUSA300HOUMR0027 bacitracin ABC ATP binding cassette transporter, ABC protein/IS431mec transposase
* * ÷ CP000731 20297 20513 217 3 [1] [1] 2 [USA300HOU_pUSA300HOUMR0027] [USA300HOU_pUSA300HOUMR0027]
* * ÷ CP000731 20765–21078 21138 61–374 2 [1] [1] 2 [USA300HOU_pUSA300HOUMR0027] [USA300HOU_pUSA300HOUMR0027]
* * ÷ CP000731 22234 22483 250 2 [1] [1] 2 USA300HOU_pUSA300HOUMR0028 macrolide transporter
* * ÷ CP000731 22524 22799 276 2 [1] [1] 2 USA300HOU_pUSA300HOUMR0028 macrolide transporter
* * ÷ CP000731 22941 23146 206 2 [1] [1] 2 [USA300HOU_pUSA300HOUMR0028]–[USA300HOU_pUSA300HOUMR0029] [USA300HOU_pUSA300HOUMR0028],[USA300HOU_pUSA300HOUMR0029]
* * ÷ CP000731 23513 24013 501 2 [1] [1] 2 [USA300HOU_pUSA300HOUMR0029] [USA300HOU_pUSA300HOUMR0029]
* * ÷ CP000731 24155 24310 156 2 [1] [0] 2 USA300HOU_pUSA300HOUMR0029/USA300HOU_pUSA300HOUMR0030 macrolide 2'‑phosphotransferase/Sin recombinase
* * ÷ CP000731 24579 24718 140 2 [1] [1] 2 USA300HOU_pUSA300HOUMR0030 Sin recombinase
* * ÷ CP000731 24860 24988 129 2 [1] [1] 3 USA300HOU_pUSA300HOUMR0030 Sin recombinase
* * ÷ CP000731 26068 26301 234 2 [1] [1] 2 [USA300HOU_pUSA300HOUMR0033] [USA300HOU_pUSA300HOUMR0033]
* * ÷ CP000731 26562 26762 201 2 [1] [1] 2 USA300HOU_pUSA300HOUMR0033 partitioning protein
* * ÷ CP000731 26893 27041 149 2 [1] [0] NA USA300HOU_pUSA300HOUMR0033/– partitioning protein/–

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? USA300TCH1516_ALE 512620 =71 (1.130)58 (1.290)
+40 bp		 42/200 0.1 53.3% 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