New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	2085296 =	16 (0.790)	14 (0.770)	11/252	0.5	42.8%	intergenic (‑558/‑400)	mapW2/USA300HOU_1944	cell surface protein MapW2/hypothetical protein
	?	CP000730	= 2128343	23 (1.270)					intergenic (+57/+1062)	int/hlgB	bacteriophage integrase/possible leukocidin subunit

AAAAAAGTTGCAACACTTGCATTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAATTTTAGGGACTTTT  >  CP000730/2085157‑2085424                                                                                                                                            |                                                                                                                                 tacatccgtgtattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTg                                                                                                                                 <  2:187854‑M1/2‑1 (MQ=255) tacatccgtgtattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTg                                                                                                                                 <  2:201001‑M1/2‑1 (MQ=255)     tccgtgcattctcatttgttagaagaaaaatttaatgaagagtacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATc                                                                                                                             >  2:214821‑M1/136‑141 (MQ=255)          gCAACACTTGCATTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAAc                                                                                                                        <  1:78557/141‑1 (MQ=255)          gCAACACTTGCATTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAAc                                                                                                                        <  2:149908/141‑1 (MQ=255)            aaCACTTGCATTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTg                                                                                                                      <  1:15709/141‑1 (MQ=255)               acTTGCATTAGCAAATTTATTATTAGTTGGTGCACTTACTGTCAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGgag                                                                                                                   >  2:202949/1‑141 (MQ=255)                     aTTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACtttt                                                                                                             <  2:191615/141‑1 (MQ=255)                          gaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACAt                                                                                                        >  2:369‑M1/115‑141 (MQ=255)                          gaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACAt                                                                                                        >  2:182077‑M1/115‑141 (MQ=255)                                aaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAAtt                                                                                                  <  1:472‑M1/33‑1 (MQ=255)                                aaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAAtt                                                                                                  <  1:216405‑M1/33‑1 (MQ=255)                                   tttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggaccccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACt                                                                                               <  2:134783‑M1/36‑1 (MQ=255)                                   tattaGTTGGTGCACTTACTGACAATAGTGCCAAAGACGAATCTAAGAAAGATGATACTGATTTGAAGCTAGTTAGTAACAACGTCTCTCTGTTAACGACCGTTTTGTATCAAAACTGGAGACTTTTAACATAAAATTACt                                                                                               >  1:89414/1‑141 (MQ=255)                                                 caaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAg                                                                                 >  1:67311‑M1/92‑141 (MQ=255)                                                  ttACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGt                                                                                <  1:14124/141‑1 (MQ=255)                                                            tAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCat                                                                      <  2:31357/141‑1 (MQ=255)                                                                       gaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGACACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGt                                                           >  1:150509‑M1/70‑141 (MQ=255)                                                                        cGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATANCAAGGtt                                                          >  2:168481/1‑141 (MQ=255)                                                                          aaTCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAAGTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTta                                                        <  2:89414/141‑1 (MQ=255)                                                                              tAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTAAAAAAAAAAAAAAAAGTAAAACAGCATAATATCAAGGTTTATAAc                                                    <  2:77797/141‑1 (MQ=255)                                                                               gtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACt                                                   >  2:472‑M1/62‑141 (MQ=255)                                                                               gtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATAATAAAAAAAGTAAAACAGCATAATATCAAGGTTTATAACt                                                   >  2:216405‑M1/62‑141 (MQ=255)                                                                                taatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACtt                                                  <  2:179960‑M1/81‑1 (MQ=255)                                                                                                 agggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAataata                                 <  1:205805‑M1/98‑1 (MQ=255)                                                                                                        tagttagtCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCata                          >  1:217841/1‑141 (MQ=255)                                                                                                        tagttagtCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCata                          >  1:84043/1‑141 (MQ=255)                                                                                                           ttagtCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATataa                       <  1:201729/141‑1 (MQ=255)                                                                                                                aataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATataaaataa                  >  1:134783‑M1/29‑141 (MQ=255)                                                                                                                         tgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAttttagg         >  2:96867‑M1/20‑141 (MQ=255)                                                                                                                         tataTGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAttttagg         <  2:214092/141‑1 (MQ=255)                                                                                                                               tacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAttttagggacttt   <  1:17111‑M1/128‑1 (MQ=255)                                                                                                                                tATCAATCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAttttagggactttt  <  1:202949/141‑1 (MQ=255)                                                                                                                                            |                                                                                                                                 AAAAAAGTTGCAACACTTGCATTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAATTTTAGGGACTTTT  >  CP000730/2085157‑2085424

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