breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation freq annotation gene description
RA 367,644 G→T 100% intergenic (‑96/‑20) nanA ← / → nagC N‑acetylneuraminate lyase/possible transcriptional regulator
RA 479,553 G→A 100% A194T (GCA→ACA)  USA300HOU_0458 → hypothetical protein
RA 512,643 A→G 50.0% intergenic (+711/‑150) recR → / → rrs1 recombination protein RecR/16S ribosomal RNA
RA 638,614 G→T 100% T14K (ACA→AAA)  thiD ← phosphomethylpyrimidine kinase
RA 790,778 G→A 100% intergenic (+277/‑197) kipA → / → ltaS possible allophanate hydrolase subunit 2/possible phosphatidylglycerol‑‑membrane‑oligosaccharide glycerophosphotransferase
RA 1,232,465 G→C 100% A124P (GCG→CCG)  prkC → non‑specific serine/threonine protein kinase
RA 1,416,458 A→T 100% I216N (ATT→AAT)  oppD ← 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 1,646,189 G→C 100% A155G (GCA→GGA)  pepP ← M24B family Xaa‑Pro dipeptidase
RA 1,744,454 C→T 100% G73D (GGC→GAC)  apt ← adenine phosphoribosyltransferase
RA 1,797,772 G→C 100% R7G (CGC→GGC)  phoR ← sensor histidine kinase
RA 2,010,363 C→T 100% C146Y (TGT→TAT)  ygaD ← ABC superfamily ATP binding cassette transporter, membrane protein
RA 2,021,817 C→T 53.2% V139I (GTT→ATT)  ykhA ← acyl‑CoA hydrolase
RA 2,279,705 G→A 100% intergenic (+1373/+6659) mtlD → / ← glmM mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase
RA 2,532,298 A→T 100% T15T (ACA→ACT)  murN → FemAB family peptidoglycan biosynthesis protein
RA 2,856,087 T→A 100% P80P (CCT→CCA)  USA300HOU_2698 → hypothetical protein

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ CP000730 58052 58148 97 2 [1] [1] 2 USA300HOU_0048/USA300HOU_0049 hypothetical membrane protein/hypothetical protein
* * ÷ CP000730 102524 102556 33 2 [1] [1] 2 USA300HOU_0103 hypothetical protein
* * ÷ CP000730 191415 191455 41 2 [1] [1] 2 USA300HOU_0180/aldH2 hypothetical membrane protein/aldehyde dehydrogenase (NAD(+))
* * ÷ CP000730 460057 460096 40 2 [1] [1] 2 hsdS1 type I site‑specific deoxyribonuclease specificity subunit
* * ÷ CP000730 708088 708154 67 2 [1] [1] 2 sirR possible metal‑dependent transcriptional regulator
* * ÷ CP000730 719339 719372 34 2 [1] [1] 2 nupC2 CNT family concentrative nucleoside transporter
* * ÷ CP000730 799039 799189 151 2 [1] [1] 2 recQ possible glycine betaine/carnitine/choline ABC superfamily ATP binding cassette transporter, membrane protein
* * ÷ CP000730 815077 815098 22 2 [1] [1] 2 sstD iron (Fe+3) ABC superfamily ATP binding cassette transporter, binding protein
* * ÷ CP000730 968773 968844 72 2 [1] [1] 2 rexA ATP‑dependent nuclease Rex subunit A
* * ÷ CP000730 987917 987970 54 3 [1] [1] 2 USA300HOU_0943/oppB1 hypothetical membrane protein/oligopeptide ABC superfamily ATP binding cassette transporter, membrane protein
* * ÷ CP000730 1165761 1165864 104 2 [1] [1] 2 USA300HOU_1092/USA300HOU_1093 hypothetical protein/hypothetical membrane protein
* * ÷ CP000730 1266857 1266940 84 3 [1] [1] 2 topA DNA topoisomerase A
* * ÷ CP000730 1307702 1307732 31 2 [1] [1] 2 USA300HOU_1214 transcriptional regulator
* * ÷ CP000730 1325645 1325729 85 2 [1] [1] 2 glpP glycerol uptake operon antiterminator
* * ÷ CP000730 1338937 1339010 74 3 [1] [1] 2 USA300HOU_1241/USA300HOU_1242 hypothetical protein/hypothetical protein
* * ÷ CP000730 1400344 1400391 48 2 [1] [1] 2 umuC ImpB/MucB/SamB family DNA‑damage repair protein
* * ÷ CP000730 1594860 1594935 76 2 [1] [1] 2 USA300HOU_1471 hypothetical bacteriophage protein
* * ÷ CP000730 1630961 1631075 115 2 [1] [1] 2 yqjA hypothetical membrane protein
* * ÷ CP000730 1632016 1632073 58 2 [1] [1] 2 [bmfBB] [bmfBB]
* * ÷ CP000730 1637802 1637865 64 2 [1] [1] 2 recN DNA repair protein RecN
* * ÷ CP000730 1678730 1678778 49 2 [1] [1] 2 recO recombination protein RecO
* * ÷ CP000730 1758704 1758813 110 2 [1] [1] 2 [USA300HOU_1649] [USA300HOU_1649]
* * ÷ CP000730 1792213 1792237 25 2 [1] [1] 2 polA DNA‑directed DNA polymerase I
* * ÷ CP000730 1824111 1824139 29 2 [1] [1] 2 [ackA] [ackA]
* * ÷ CP000730 1898515 1898595 81 2 [1] [1] 2 ribD diaminohydroxyphosphoribosylaminopyrimidine deaminase
* * ÷ CP000730 1907636 1907682 47 2 [1] [1] 2 USA300HOU_1769 hypothetical protein
* * ÷ CP000730 1947682 1947829 148 2 [1] [1] 2 epiE epidermin ABC superfamily ATP binding cassette transporter, membrane protein
* * ÷ CP000730 1977116 1977171 56 2 [0] [1] 2 yhaN hypothetical protein
* * ÷ CP000730 1982465 1982533 69 2 [1] [1] 2 USA300HOU_1843 sensor histidine kinase
* * ÷ CP000730 2125707 2125728 22 2 [1] [1] 2 USA300HOU_2006 hypothetical bacteriophage protein
* * ÷ CP000730 2176704–2179433 2181106–2179436 4–4403 2 [1] [1] 2 [rrl4]–[rrs4] [rrl4],[rrs4]
* * ÷ CP000730 2220469 2220486 18 3 [0] [0] 3 USA300HOU_2091/atpC hypothetical protein/F‑ATPase superfamily proton(H+)‑ or sodium (Na+)‑translocating F‑type ATPase epsilon subunit
* * ÷ CP000730 2419048 2419079 32 2 [1] [1] 2 odh D‑octopine dehydrogenase
* * ÷ CP000730 2849412 2849435 24 2 [1] [1] 2 ybfQ rhodanese domain sulfurtransferase

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP000730 512620 =13 (1.450)6 (1.030)
+45 bp		 6/170 NT 45.6% intergenic (+688/‑173) recR/rrs1 recombination protein RecR/16S ribosomal RNA
?CP000730 = 517814 9 (1.010)noncoding (114/114 nt) rrf1 5S ribosomal RNA