New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	2085296 =	19 (0.640)	4 (0.150)	4/232	NT	17.4%	intergenic (‑558/‑400)	mapW2/USA300HOU_1944	cell surface protein MapW2/hypothetical protein
	?	CP000730	= 2128343	21 (0.790)					intergenic (+57/+1062)	int/USA300HOU_2011	bacteriophage integrase/possible leukocidin subunit

ACATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGA‑CAAATTATTAAGTAATGTGAAAAAAG  >  CP000730/2128206‑2128481                                                                                                                                          |                                                                                                                                            aCATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgt                                                                                                                                          <  2:181835‑M2/141‑4 (MQ=255)  cATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgta                                                                                                                                         <  1:233885‑M2/141‑5 (MQ=255)    tCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatc                                                                                                                                       >  2:316219‑M2/1‑135 (MQ=255)         gtATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaac                                                                                                                                  <  1:19937‑M2/141‑12 (MQ=255)              ctcATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTATAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTgggg                                                                                                                             >  1:43247/1‑141 (MQ=255)                 aTTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACACACTAACTACTGTTGTGACAAGGTTTCTAtgtatccaaactggagact                                                                                                                          <  2:162160‑M2/141‑20 (MQ=255)                         aaagaaAAATATAAGGAAGAGGACAAAAAAACAACTAAACTTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAAc                                                                                                                  <  2:46689/140‑1 (MQ=255)                                   ttAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattactt                                                                                                        <  2:353944‑M2/141‑38 (MQ=255)                                        gAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCAGATTTAATCg                                                                                                   >  2:30413/1‑141 (MQ=255)                                                   aaaaaCAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAAtcttct                                                                                        >  1:197531/1‑141 (MQ=255)                                                          acTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTa                                                                                 >  2:112324/1‑141 (MQ=255)                                                                 ttttAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAaataa                                                                          <  2:275036/141‑1 (MQ=255)                                                                 ttttAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACAGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAaataa                                                                          <  2:19893/141‑1 (MQ=255)                                                                 tcttAGAAAGTTTGCAATTGAGGGACCCATTAGGGACTCCAAACCCCACAAATGCTGGTGTTACAAGGTTTCTATGTTCCCAAACTGGGGGCAAGTTTAACGAGCTGATTTAATCGGACAATCTTCTTATATTAAAaataa                                                                          <  2:19877/139‑1 (MQ=255)                                                                     acaaaGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAatgat                                                                      <  2:276268/139‑1 (MQ=255)                                                                     aGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAatgat                                                                      >  1:84609/1‑141 (MQ=255)                                                                          gTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttat                                                                 >  1:181835‑M2/1‑65 (MQ=255)                                                                               tAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAatat                                                            <  2:19937/141‑1 (MQ=255)                                                                                aaTTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGAAGTTGTAAGAtt                                                           >  2:213823/1‑141 (MQ=255)                                                                                       ggACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGaa                                                    <  2:217175/141‑1 (MQ=255)                                                                                             aTTAGGGCCTCCAAAACCAATAACTAATGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaata                                              >  1:162160‑M2/1‑46 (MQ=255)                                                                                              ttAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCTGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTg                                             >  1:81967/1‑141 (MQ=255)                                                                                                   gACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAAt                                        <  2:43247/141‑1 (MQ=255)                                                                                                    aatccATACCCAATAAATCCTGTTGTTACAAGGTTTCTAtgtagccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataatacctc                                       >  2:341024‑M2/3‑39 (MQ=255)                                                                                                           aCCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATc                                >  1:218856/1‑141 (MQ=255)                                                                                                                ataaacaCTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGA‑Ca                          <  1:61319/141‑1 (MQ=255)                                                                                                                 taaataCCGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGA‑Caa                         <  1:64469/141‑1 (MQ=255)                                                                                                                        tgttgtTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGA‑CAAAttatta                  >  2:154096/1‑141 (MQ=255)                                                                                                                         gttgttACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCACCAGA‑CAAATTATTaa                 >  2:347890/1‑141 (MQ=255)                                                                                                                                 aaGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCCGA‑CAAATTATTAAGTAAtctg         >  2:122142/1‑141 (MQ=255)                                                                                                                                 aaGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATGTAATCGAACAATCTTCTTATCTTAAAAATAATGATGTCGTAATATTCACTAAAGCATTTGATCATCGTGCAT‑AGACCACATCATCAAGTAAtgtg         >  2:176805/1‑141 (MQ=255)                                                                                                                                        cgaTGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGA‑CAAATTATTAAGTAATGTGAAAAAAg  <  2:265799/139‑1 (MQ=255)                                                                                                                                          |                                                                                                                                            ACATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGA‑CAAATTATTAAGTAATGTGAAAAAAG  >  CP000730/2128206‑2128481

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ 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.