New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 705329	36 (1.040)	3 (0.090)	3/242	NT	7.6%	intergenic (+1079/+81)	nhaK_1/mntA	Sodium, potassium, lithium and rubidium/H(+) antiporter/Manganese‑binding lipoprotein MntA
	?	USA300TCH1516_ALE	= 705368	39 (1.210)					intergenic (+1118/+42)	nhaK_1/mntA	Sodium, potassium, lithium and rubidium/H(+) antiporter/Manganese‑binding lipoprotein MntA

ACTTCTAGCTTTTCTCTTTCGTTCAAAGAGAAGTTCTAATACCACCATATCGTGCGATCGGGAACGGTATATATATTAATAGGAGGGTAATATATATTTAACGCACGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/705185‑705329 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atgttgatgCAACCTAAAATATTGGTATCTCCAATATTTTAGGCCACACATCAACATAACAAAGTCGAAGGCTAATAGTCCCATATCGTGCGTTAAATATATATTACCCTCCTATTAATATATATACCGTTCCCGATCGCACGATA  <  USA300TCH1516_ALE/705368‑705232                                                                                                                                                                                                                                                                                            ACTTCTAGTTTTTTTATTTAGTTCAAATAGAAGTTCTAATACCACCATATCGTGCGATCGGGAACGGTATATATATTAATAGGAGGGTAATATATATTTAACGCACGATATGGGACTATTAGCCTTCGACTTTGTTATGTT                                                                                                                                               <  2:345333/141‑1                   TCGTTCAAAGAGAAGTTCTAATACCACCATATCGTGCGATCGGGAACGGTATATATATTAATAGGAGGGTAATATATATTTAACGCACGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGCAACCTAAAATATT                                                                                                                             >  2:29207/1‑141                                                   CGTGCGATCGGGAACGGTATATATATTAATAGGAGGGTAATATATATTTAACGCACGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGCAACCTAAAATATTGGTATCTCCAATATTTTAGGCCACACATCAAC                                                                                             <  1:29207/141‑1                                                     TGCGATCGGGAACGGTATATATATTAATAGGAGGGTAATATATATTTAACGCACGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGCAACCTAAAATATTGGTATCTCCAATATTTTAGGCCACACATCAACAT                                                                                           <  2:391434/141‑1                                                                                                                                         ATGTTGATGCAACCTAAAATATTGGTATCTCCAATATTTTAGGCCACACATCAACATAACAAAGTCGAAGGCTAATAGTCCCATATCGTGCGTTAAATATATATTACCCTCCTATTAATATATATACCGTTCCCGATagaa       >  2:310260/1‑137                                                                                                                                           GTTGATGCAACCTAAAATATTGGTATCTCCAATATTTTAGGCCACACATCAACATAACAAAGTCGAAGGCTAATAGTCCCATATCGTGCGTTAAATATATATTACCCTCCTATTAATATATATACCGTTCCCGATCGCACG     <  2:305529/141‑1                                                                                                                                            TTGATGCAACCTAAAATATTGGTATCTCCAATATTTTAGGCCACACATCAACATAACAAAGTCGAAGGCTAATAGTCCCATATCGTGCGTTAAATATATATTACCCTCCTATTAATATATATACCGTTCCCGATCGCACGA    <  2:397555/141‑1                                                                                                                                             TGATGCAACCTAAAATATTGGTATCTCCAATATTTTAGGCCACACATCAACATAACAAAGTCGAAGGCTAATAGTCCCATATCGTGCGTTAAATATATATTACCCTCCTATTAATATATATACCGTTCCCGATCGCACGAT   <  2:393864/141‑1                                                                                                                                              GATGCAACCTAAAATATTGGTATCTCCAATATATTAGGCCACACATCAACATAACAAAGTCGAAGGCTAATAGACCCATATCGTGCGTTAAATATATATTACCCTCCTATTAATATATATACCGTTCCCGATCGCACGATA  >  2:379197/1‑141                                                                                                                                                                                                                                                                                            ACTTCTAGCTTTTCTCTTTCGTTCAAAGAGAAGTTCTAATACCACCATATCGTGCGATCGGGAACGGTATATATATTAATAGGAGGGTAATATATATTTAACGCACGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/705185‑705329 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atgttgatgCAACCTAAAATATTGGTATCTCCAATATTTTAGGCCACACATCAACATAACAAAGTCGAAGGCTAATAGTCCCATATCGTGCGTTAAATATATATTACCCTCCTATTAATATATATACCGTTCCCGATCGCACGATA  <  USA300TCH1516_ALE/705368‑705232

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.