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

AAAAAAGTTGCAACACTTGCATTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAATTTTAGGGACTTTTTAGGGACT  >  CP000730/2085157‑2085432                                                                                                                                            |                                                                                                                                         aaaaaaGTTGCAACACTTGCATTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACAGTTTTg                                                                                                                                         >  1:4320/1‑141 (MQ=255)  acatccgtgtattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGt                                                                                                                                        <  2:181835‑M1/3‑1 (MQ=255)   catccgtgtattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTa                                                                                                                                       <  1:233885‑M1/4‑1 (MQ=255)     tccgtgtattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATc                                                                                                                                     >  2:316219‑M1/136‑141 (MQ=255)          gtattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAAc                                                                                                                                <  1:19937‑M1/11‑1 (MQ=255)           cAACACTTGCATTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACt                                                                                                                               <  1:33031/141‑1 (MQ=255)               acTTGCATTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGgag                                                                                                                           <  1:78048/141‑1 (MQ=255)                  atttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacacactaactactgttgtgacaaggtttctaTGTATCCAAACTGGAGACt                                                                                                                        <  2:162160‑M1/19‑1 (MQ=255)                          cAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACAt                                                                                                                <  1:334489/141‑1 (MQ=255)                             aTTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATaaa                                                                                                             <  1:193283/141‑1 (MQ=255)                               ttattattaGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAAt                                                                                                           <  2:250752/141‑1 (MQ=255)                                    ttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACtt                                                                                                      <  2:353944‑M1/37‑1 (MQ=255)                                    attaGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACtt                                                                                                      >  1:107526/1‑141 (MQ=255)                                               cACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTCTCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCaaaa                                                                                           >  2:154400/1‑141 (MQ=255)                                                           aTAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCa                                                                               <  2:151396/141‑1 (MQ=255)                                                                 ccAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAatat                                                                         >  1:63435/1‑141 (MQ=255)                                                                     aGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAg                                                                     >  1:252770/1‑141 (MQ=255)                                                                     aGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAg                                                                     >  1:252915/1‑141 (MQ=255)                                                                      gCCGAATCTAAGAAAGATTATACTGATTTGAAGTTAGTCAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAgg                                                                    <  1:242423/141‑1 (MQ=255)                                                                      gCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAgg                                                                    <  1:305408/141‑1 (MQ=255)                                                                           gtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTtat                                                               >  1:181835‑M1/66‑141 (MQ=255)                                                                                   aagaTGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTttat                                                       <  1:201668/141‑1 (MQ=255)                                                                                       tgatACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTttatcatt                                                   >  1:280254/1‑141 (MQ=255)                                                                                         atACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTCTCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTttatcattat                                                 >  2:225556/1‑141 (MQ=255)                                                                                              attagggcctccaaaaccaataactaatgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCaata                                            >  1:162160‑M1/47‑141 (MQ=255)                                                                                                     aatccatacccaataaatcctgttgttacaaggtttctaTGTAGCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTc                                     >  2:341024‑M1/40‑141 (MQ=255)                                                                                                                       tttATATGTTATCGACCGTTTTGTAACCAAACAGGAGACTTTAACCATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAtttta                   <  2:267907/141‑1 (MQ=255)                                                                                                                            atGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAttttagggac              <  1:189338/141‑1 (MQ=255)                                                                                                                                      ccGTTTTGTCTCCAAACTGAAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATGATACCTCATATAAAATAAAAttttagggactttttagggc    >  1:158851/1‑140 (MQ=255)                                                                                                                                       cGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAttttagggactttttagggac   >  2:317989/1‑141 (MQ=255)                                                                                                                                        ttgttGTATCCAAACTGGACACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTGTATCATTATCAATAATCCCTCATATAAAATAAAAtgttagggactttttagggact  <  1:53010/138‑1 (MQ=255)                                                                                                                                            |                                                                                                                                         AAAAAAGTTGCAACACTTGCATTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAATTTTAGGGACTTTTTAGGGACT  >  CP000730/2085157‑2085432

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.