New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	= 2085309	13 (0.420)	6 (0.220)	6/230	NT	27.5%	intergenic (‑571/‑387)	mapW2/USA300HOU_1944	cell surface protein MapW2/hypothetical protein
	?	CP000730	2128358 =	20 (0.730)					intergenic (+72/+1047)	int/hlgB	bacteriophage integrase/possible leukocidin subunit

ATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAAAGAATATCCTTATCAAA  >  CP000730/2128222‑2128496                                                                                                                                         |                                                                                                                                           aTTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGc                                                                                                                                         <  1:331930/140‑1 (MQ=255)     gtaccaaatttattagtagttggtgtgcttactgacactagtgccaaagccgaatctaagaaagatgatactgatttgaagttagttagtcataacgtttatatgttatcgaccgttttgtatccaaactggGGGCAata                                                                                                                                     <  2:81047‑M2/8‑1 (MQ=255)      ttAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAatat                                                                                                                                    >  1:179699/1‑140 (MQ=255)          aagaaAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAAc                                                                                                                                <  2:311541/140‑1 (MQ=255)          aagaaAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAAc                                                                                                                                <  1:340341/140‑1 (MQ=255)               aaaTTTAATGAAGATGACAAAAAAACAACTAAAATCTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAACCCCAATAAATCCTGTTGTTACAAGTGTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCt                                                                                                                           <  1:209981/140‑1 (MQ=255)                   ttAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGAtt                                                                                                                       >  1:284348/1‑140 (MQ=255)                   ttAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCAATGTATCAAAACTGGGGACAATATAAACGCGCTGAtt                                                                                                                       >  1:132416/1‑140 (MQ=255)                         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)                                cttactgacaatagtgacaaagccgaatctaagaaagatgatactgatttgaagttagttagtcataacgtttatatgttatcgaccgttttgtatccaaactggGGGCAATATAAACGCGCTGATTTAATCGGACAAtc                                                                                                          <  2:44665‑M2/35‑1 (MQ=255)                                          atagtgccaaagccgaatctaagaaagatgatactgatttgaagatagttagtcataacgtttatatgtgatcgaccgttttgtatacaaactggGGGCAATATAAACGCGCTGATTTAATCGGAAAAACTACTTGTAtt                                                                                                >  2:34939‑M2/96‑140 (MQ=255)                                                     aGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAAGATAAACGCGCTGAGTGAATCGGACAATCTTCTTATATTAAAAATAatga                                                                                     >  1:119170/1‑140 (MQ=255)                                                               tAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAata                                                                           <  1:147990/140‑1 (MQ=255)                                                                       ggACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATCATGATGTCGTAATATTTCATGa                                                                   >  1:335449/1‑140 (MQ=255)                                                                       gatactgatttgaagttagttagtcataacgtttatatgttatcgaccgttttgtatccacactggGGGCAATATAAACGCGCGGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGa                                                                   >  2:310326‑M2/67‑140 (MQ=255)                                                                        gACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGaa                                                                  >  2:85811/1‑140 (MQ=255)                                                                           cggatttgtagttagttagtcataacgtttatattttatcgaccgtgttgtatccaaactggGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCa                                                               <  1:118490‑M2/78‑1 (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)                                                                                                                     ccgttttgtatccaaactggGGGCAATATAAACGCGCTGATTTAATCGGACCATGTTCGAAAATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGaaa                     <  1:350536‑M2/120‑1 (MQ=255)                                                                                                                       gcgaTGTATCCAAAGTGGGGGCAACATAAACGCGCTGATTTAATCGGACAATCGTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGaaaaa                   <  2:284348/137‑1 (MQ=255)                                                                                                                        cTATGTATCCAAACGGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTAATAATAGTGCATCAGACAAATTATTAAGTAATGTTaaaaaa                  >  2:16983/1‑140 (MQ=255)                                                                                                                          aTGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATAATGAGCTAAAATGCAATGAAGCATTTGATCATGGTGCATCAGACAAATTATTAAGTAATGTGAGAAAAGa                >  1:169471/1‑140 (MQ=255)                                                                                                                             tatccaaactggGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAACATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATAAGACAAATTAATAATTAATGTGAAAAAAGAata             >  1:298356‑M2/13‑140 (MQ=255)                                                                                                                                 caaactggGGGCAATATAAACGCGCTAATTTAATCGGACAAACTACTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAAAGAATATCCt         <  1:67993‑M2/132‑1 (MQ=255)                                                                                                                                   aactggGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTCTTAAGTAATGTGAAAAAAGAATATCCTTa       >  2:329639‑M2/7‑140 (MQ=255)                                                                                                                                       ggGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAAAGAATATCCTTATCaa   <  1:16990‑M2/138‑1 (MQ=255)                                                                                                                                        gGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAAAGAATATCCTTATCaaa  >  1:233364‑M2/2‑140 (MQ=255)                                                                                                                                         |                                                                                                                                           ATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAAAGAATATCCTTATCAAA  >  CP000730/2128222‑2128496

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.