breseq  version 0.32.1  revision 5f2cb669173e
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation freq annotation gene description
RA 8,822 A→T 10.6% E597D (GAA→GAT gyrA → DNA topoisomerase (ATP‑hydrolyzing) subunit A
RA 39,378 C→A 100% D586Y (GAT→TAT)  mecA ← penicillin binding protein 2 prime
RA 110,660 T→A 14.3% I173I (ATT→ATA USA300HOU_0109 → staphylococcal tandem lipoprotein
RA 111,512 A→G 27.7% S194S (TCA→TCG USA300HOU_0110 → possible staphylococcal tandem lipoprotein
RA 111,516 C→A 29.2% Q196K (CAA→AAA)  USA300HOU_0110 → possible staphylococcal tandem lipoprotein
RA 111,560 T→C 18.6% R210R (CGT→CGC USA300HOU_0110 → possible staphylococcal tandem lipoprotein
RA 367,644 G→T 100% intergenic (‑96/‑20) nanA ← / → USA300HOU_0336 N‑acetylneuraminate lyase/possible transcriptional regulator
RA 408,719 T→C 16.6% L491L (TTA→TTG metE ← 5‑methyltetrahydropteroyltriglutamate‑‑ homocysteine S‑methyltransferase
RA 479,553 G→A 100% A194T (GCA→ACA)  USA300HOU_0458 → hypothetical protein
RA 512,643 A→G 51.0% intergenic (+711/‑150) recR → / → rrs1 recombination protein RecR/16S ribosomal RNA
RA 638,614 G→T 100% T14K (ACA→AAA)  thiD ← phosphomethylpyrimidine kinase
RA 707,879 A→T 100% L11I (TTA→ATA)  USA300HOU_0653 ← ABC superfamily ATP binding cassette transporter, ABC protein
RA 790,778 G→A 100% intergenic (+277/‑197) USA300HOU_0741 → / → USA300HOU_0742 possible allophanate hydrolase subunit 2/possible phosphatidylglycerol‑‑membrane‑oligosaccharide glycerophosphotransferase
RA 1,064,126 G→C 100% Y121* (TAC→TAG USA300HOU_1000 ← LytR family transcriptional regulator
RA 1,232,465 G→C 100% A124P (GCG→CCG)  USA300HOU_1157 → non‑specific serine/threonine protein kinase
RA 1,238,307 C→T 100% Q141* (CAA→TAA)  USA300HOU_1162 → glycerone kinase
RA 1,274,212 A→T 100% K205N (AAA→AAT USA300HOU_1186 → CodY family transcriptional regulator
RA 1,318,237 T→A 100% F124Y (TTT→TAT)  miaB → 2‑methylthioadenine synthetase
RA 1,345,220 A→G 18.8% intergenic (+32/‑18) USA300HOU_1256 → / → USA300HOU_1257 hypothetical protein/hypothetical protein
RA 1,416,458 A→T 100% I216N (ATT→AAT)  USA300HOU_1314 ← oligopeptide ABC superfamily ATP binding cassette transporter, ABC protein
RA 1,440,007 Δ1 bp 100% coding (34/201 nt) cspA ← cold shock protein CspA
RA 1,474,639 C→G 100% A9129P (GCA→CCA)  ebh ← extracellular matrix binding protein
RA 1,481,355 G→T 100% A6890E (GCA→GAA)  ebh ← extracellular matrix binding protein
RA 1,513,930 A→T 100% L413F (TTA→TTT USA300HOU_1379 → hypothetical membrane protein
RA 1,555,359 A→G 13.8% intergenic (+55/+51) fer → / ← USA300HOU_1423 ferredoxin/hypothetical membrane protein
RA 1,607,132 C→T 100% intergenic (+1247/+815) USA300HOU_1490 → / ← USA300HOU_1492 integrase/possible lipoprotein
RA 1,644,319 C→T 8.7% K72K (AAG→AAA accB ← biotin carboxyl carrier subunit
RA 1,646,189 G→C 100% A155G (GCA→GGA)  USA300HOU_1531 ← M24B family Xaa‑Pro dipeptidase
RA 1,744,454 C→T 100% G73D (GGC→GAC)  apt ← adenine phosphoribosyltransferase
RA 1,770,911 T→A 100% S73C (AGT→TGT)  hemD ← uroporphyrinogen‑III synthase
RA 1,797,772 G→C 100% R7G (CGC→GGC)  USA300HOU_1679 ← sensor histidine kinase
RA 1,805,508 C→T 50.0% G535S (GGT→AGT)  pykA ← pyruvate kinase
RA 1,883,654 C→T 100% G522D (GGT→GAT)  fmtB1 ← cell surface anchored protein
RA 2,010,363 C→T 100% C146Y (TGT→TAT)  USA300HOU_1861 ← ABC superfamily ATP binding cassette transporter, membrane protein
RA 2,018,733:1 (A)6→7 100% coding (186/810 nt) USA300HOU_1869 ← transglycosylase
RA 2,143,110 G→A 100% V163V (GTG→GTA USA300HOU_2026 → hypothetical membrane protein
RA 2,205,303 G→A 15.4% L273F (CTT→TTT)  ddlA ← D‑alanine‑‑D‑alanine ligase
RA 2,274,965 G→C 100% E106D (GAG→GAC bglG → transcriptional antiterminator
RA 2,279,705 G→A 100% intergenic (+1373/+6659) mtlD → / ← glmM mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase
RA 2,315,088 T→A 100% K61I (AAA→ATA)  USA300HOU_2172 ← MFS family major facilitator transporter
RA 2,342,380 A→C 100% L78V (TTG→GTG)  USA300HOU_2199 ← possible HAD superfamily hydrolase
RA 2,388,866 A→G 100% G8G (GGA→GGG USA300HOU_2249 → hypothetical protein
RA 2,504,889 G→A 13.5% intergenic (+193/+211) USA300HOU_2365 → / ← gltT hypothetical protein/DAACS family dicarboxylate/amino acid:sodium (Na+) or proton (H+) symporter
RA 2,504,894 C→T 18.0% intergenic (+198/+206) USA300HOU_2365 → / ← gltT hypothetical protein/DAACS family dicarboxylate/amino acid:sodium (Na+) or proton (H+) symporter
RA 2,504,896 G→C 16.8% intergenic (+200/+204) USA300HOU_2365 → / ← gltT hypothetical protein/DAACS family dicarboxylate/amino acid:sodium (Na+) or proton (H+) symporter
RA 2,504,957 G→C 11.7% intergenic (+261/+143) USA300HOU_2365 → / ← gltT hypothetical protein/DAACS family dicarboxylate/amino acid:sodium (Na+) or proton (H+) symporter
RA 2,504,989 T→C 10.0% intergenic (+293/+111) USA300HOU_2365 → / ← gltT hypothetical protein/DAACS family dicarboxylate/amino acid:sodium (Na+) or proton (H+) symporter
RA 2,532,298 A→T 100% T15T (ACA→ACT USA300HOU_2392 → FemAB family peptidoglycan biosynthesis protein
RA 2,679,650 G→A 100% C45Y (TGT→TAT)  USA300HOU_2536 → possible secretory antigen
RA 2,709,600 (T)5→4 100% coding (1327/1812 nt) USA300HOU_2562 ← possible acetyltransferase
RA 2,856,087 T→A 100% P80P (CCT→CCA USA300HOU_2698 → hypothetical protein

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP000730 512620 =20 (0.800)16 (0.990)
+45 bp
13/170 NT 45.0% intergenic (+688/‑173) recR/rrs1 recombination protein RecR/16S ribosomal RNA
?CP000730 2176447 = 40 (1.610)noncoding (114/114 nt) rrf5 5S ribosomal RNA