New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	2085296 =	15 (0.490)	4 (0.150)	4/230	NT	19.3%	intergenic (‑558/‑400)	mapW2/USA300HOU_1944	cell surface protein MapW2/hypothetical protein
	?	CP000730	= 2128343	20 (0.730)					intergenic (+57/+1062)	int/USA300HOU_2011	bacteriophage integrase/possible leukocidin subunit

CTACATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAAAGA  >  CP000730/2128204‑2128482                                                                                                                                            |                                                                                                                                            cTACATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTAAAAGGTTTCTa                                                                                                                                             >  1:216443/1‑140 (MQ=255) cTACATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAACAAGGCGGACAAAAAAAGAAATAACATGTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAAACCAATAAATACTGTTGTTACAAGGGTTCTa                                                                                                                                             >  2:163092/1‑140 (MQ=255)    cATCCGTGTATTCTCATTTGGTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgt                                                                                                                                          <  2:269632‑M2/140‑4 (MQ=255)       ccGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTAGAAGGTTTCTAtgtatc                                                                                                                                       <  1:297600‑M2/140‑7 (MQ=255)          tgtATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaa                                                                                                                                    <  1:357613‑M2/140‑10 (MQ=255)            tATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaac                                                                                                                                  >  1:149427‑M2/1‑129 (MQ=255)            tATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaac                                                                                                                                  >  2:248277‑M2/1‑129 (MQ=255)                ctcATCTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTAAGAAAGTATGTAATTTAGGCACCCACTAGGGACTCCAACCCCAATAAATACTGTTGTTACAAGGATTCTAtgtgtccaacacggg                                                                                                                              <  2:36317‑M2/140‑16 (MQ=255)                   aTTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGc                                                                                                                           <  1:331930/140‑1 (MQ=255)                        ttAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAatat                                                                                                                      >  1:179699/1‑140 (MQ=255)                            aagaaAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAAc                                                                                                                  <  1:340341/140‑1 (MQ=255)                            aagaaAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAAc                                                                                                                  <  2:311541/140‑1 (MQ=255)                                 aaaTTTAATGAAGATGACAAAAAAACAACTAAAATCTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAACCCCAATAAATCCTGTTGTTACAAGTGTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCt                                                                                                             <  1:209981/140‑1 (MQ=255)                                     ttAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGAtt                                                                                                         >  1:284348/1‑140 (MQ=255)                                     ttAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCAATGTATCAAAACTGGGGACAATATAAACGCGCTGAtt                                                                                                         >  1:132416/1‑140 (MQ=255)                                           aaGAGGACAAAAAAACAACTAAAGTTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcat                                                                                                   >  2:102845‑M2/1‑98 (MQ=255)                                           aaGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCg                                                                                                   <  1:128925/140‑1 (MQ=255)                                            agagGACAAAAAAACAACTAAAATTTTTGAAAGTATGTAATTTAGGGACCCTTTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCgg                                                                                                  <  1:319343/140‑1 (MQ=255)                                            agagGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCgg                                                                                                  <  2:48527/140‑1 (MQ=255)                                                gACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACaa                                                                                              <  2:330245/140‑1 (MQ=255)                                                                       aGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAAGATAAACGCGCTGAGTGAATCGGACAATCTTCTTATATTAAAAATAatga                                                                       >  1:119170/1‑140 (MQ=255)                                                                          aaGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaacaagtaaaacagcataatatcaagttt                                                                    <  1:151492‑M2/140‑74 (MQ=255)                                                                             tATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttat                                                                 >  2:207118‑M2/1‑64 (MQ=255)                                                                                 tAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAata                                                             <  1:147990/140‑1 (MQ=255)                                                                                         ggACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATCATGATGTCGTAATATTTCATGa                                                     >  1:335449/1‑140 (MQ=255)                                                                                          gACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGaa                                                    >  2:85811/1‑140 (MQ=255)                                                                                             ccATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatca                                                 >  1:39191‑M2/1‑48 (MQ=255)                                                                                                      aCTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAAt                                        >  1:220222/1‑140 (MQ=255)                                                                                                           aaaCCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGc                                   >  1:324509/1‑140 (MQ=255)                                                                                                             aCCCAAGAAATACTGGTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAACCGCGCTGATTTAATCGGACAATTTTCTTAGATTAAAAATAATGATGTCGTAATATTGAATGAAGCATTTGATAATGGTGCAt                                 <  2:139039/140‑1 (MQ=255)                                                                                                                cAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCAACAg                              >  2:110889/1‑140 (MQ=255)                                                                                                                   tcaataCTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACa                           <  1:25006/138‑1 (MQ=255)                                                                                                                   taaataCTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGAAAATGGTGCATCAGACa                           >  1:333407/1‑140 (MQ=255)                                                                                                                                         gcgaTGTATCCAAAGTGGGGGCAACATAAACGCGCTGATTTAATCGGACAATCGTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGaaaaa     <  2:284348/137‑1 (MQ=255)                                                                                                                                          cTATGTATCCAAACGGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTAATAATAGTGCATCAGACAAATTATTAAGTAATGTTaaaaaa    >  2:16983/1‑140 (MQ=255)                                                                                                                                            aTGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATAATGAGCTAAAATGCAATGAAGCATTTGATCATGGTGCATCAGACAAATTATTAAGTAATGTGAGAAAAGa  >  1:169471/1‑140 (MQ=255)                                                                                                                                            |                                                                                                                                            CTACATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAAAGA  >  CP000730/2128204‑2128482

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ 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.