New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2085296 =	40 (1.220)	6 (0.200)	6/232	NT	15.5%	coding (173/201 nt)	hlb_1	Phospholipase C
	?	USA300TCH1516_ALE	= 2128343	30 (1.020)					coding (1/825 nt)	hlb_2	Phospholipase C

ACATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAAAGA  >  USA300TCH1516_ALE/2128206‑2128482                                                                                                                                          |                                                                                                                                            aCATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgt                                                                                                                                          <  2:184800‑M2/141‑4 (MQ=255) aCATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgt                                                                                                                                          <  1:319185‑M2/141‑4 (MQ=255) aCATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTATCTAtgt                                                                                                                                          <  1:304834‑M2/141‑4 (MQ=255) aCATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTATTGTTACAAGGTGTCTAtgt                                                                                                                                          <  1:149958‑M2/141‑4 (MQ=255)  cATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgta                                                                                                                                         <  1:248249‑M2/141‑5 (MQ=255)   aTCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtat                                                                                                                                        <  1:267253‑M2/141‑6 (MQ=255)       gtgtATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAACCCCAATAAATACTGTTGTTACAAGGTGTCTAtatatccaa                                                                                                                                    <  2:200771‑M2/141‑10 (MQ=255)            ttCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactgg                                                                                                                               <  1:141066‑M2/141‑15 (MQ=255)               tcATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACTAGGTTTCTATGTATCCAAACTggggg                                                                                                                            <  2:247474/141‑1 (MQ=255)                    tGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAata                                                                                                                       <  1:20966/141‑1 (MQ=255)                          aagaaAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAAcg                                                                                                                 <  2:66168/141‑1 (MQ=255)                            gaaAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAAcgcg                                                                                                               <  2:186329/141‑1 (MQ=255)                                  tttAATGAAGAGGACAAAAAAACAACTATCATTATAGAAATGATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGAtt                                                                                                         <  1:171200/141‑1 (MQ=255)                                   ttAATGAAGAGGACAAAAAAACAACTACAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACGGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGAttt                                                                                                        <  1:34517/141‑1 (MQ=255)                                         aaGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCgg                                                                                                  >  1:44943/1‑141 (MQ=255)                                           gagGACAAAAAAACCACTCAAATTGGATAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattca                                                                                                <  1:293686‑M2/141‑46 (MQ=255)                                           gagGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattca                                                                                                >  2:248994‑M2/1‑96 (MQ=255)                                                  aaaaaaCAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCTATTAGGTACTCCAAACCCAATAAATAATGTTGGTACACGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagta                                                                                         >  1:393166‑M2/1‑89 (MQ=255)                                                   aaaaaCAACTAAAATGTTAGAAAGTATGTAATGTAGGGACCCATTAGGGACTCCAAGCCCAATAAATACTGTTGTTACAAGGCTTCTATGTATCCAAACTGGGGGTAATATAAACTCGCTGATTTGATCGGACAAtcttct                                                                                        <  1:200771/141‑1 (MQ=255)                                                     aaaCAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTta                                                                                      <  2:341638/141‑1 (MQ=255)                                                       acaacTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTtata                                                                                    >  1:3012/1‑141 (MQ=255)                                                       acaacTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTtata                                                                                    <  2:211638/141‑1 (MQ=255)                                                         aacTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATAtt                                                                                  >  2:53917/1‑141 (MQ=255)                                                         aacTAAAAATTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTTACCAAACTGGGGGCCATATAAACGCGCTGATTTAATCGGACAATCTTCTTATAtt                                                                                  >  2:294162/1‑141 (MQ=255)                                                          acTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAACCCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCGAAAATGGGCGCTATATATACGCGCTGAGTTCATCGGCCAATCTCGTTATATTa                                                                                 >  1:350890/1‑141 (MQ=255)                                                          acTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAACCTTCTTACATTa                                                                                 >  2:79944/1‑141 (MQ=255)                                                          acTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACGGGGGGCAATATAAACGCGCTGATTTGATGGGAGAATATTGTTATAGTa                                                                                 >  1:61543/1‑141 (MQ=255)                                                                      gAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAatgatg                                                                     <  2:44943/141‑1 (MQ=255)                                                                        aaGTATGTAATGTAGGAACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAGGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTc                                                                   <  1:311771/141‑1 (MQ=255)                                                                          gTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGt                                                                 <  1:326651/141‑1 (MQ=255)                                                                                aaTTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTCACAAGGTTTCTATGTATCCAAACTGGGGGCCATATAAACGCGCTGATTTAATCGGACAATCTTGTTATATTAAAAATAATTATGTCGTaaaagt                                                           >  2:253968/1‑137 (MQ=255)                                                                                      gggACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGa                                                     >  2:371381/1‑141 (MQ=255)                                                                                              ttAGGGACTCCAAACCCAGTAAATACTGTTGTTACAAGGTTTCTATGTATCCACACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGACGTAATATTCAATGAAGCATTTg                                             >  2:61154/1‑141 (MQ=255)                                                                                                aGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGAt                                           >  1:116463/1‑141 (MQ=255)                                                                                                     cTCCAAACCCAATAAATCCGGTCGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATgg                                      <  1:288641/141‑1 (MQ=255)                                                                                                     cTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATTATGTCGTAATATTCAATGAAGCATTTGATAATgg                                      <  1:191938/141‑1 (MQ=255)                                                                                                     cTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATgg                                      <  1:117643/141‑1 (MQ=255)                                                                                                        cAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGc                                   <  2:248249/141‑1 (MQ=255)                                                                                                                 caaatacTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataatacctcatataaaataaaa                          >  2:231909‑M2/2‑26 (MQ=255)                                                                                                                   aataCTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacgtatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattataactaatacctcatcttaaataaaatt                        >  2:233067‑M2/1‑24 (MQ=255)                                                                                                                   aataCTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAat                        <  2:304834/141‑1 (MQ=255)                                                                                                                           tgttACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGt                <  1:122206/141‑1 (MQ=255)                                                                                                                            gttACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataatacctcatataaaataaaattttagtgact               <  2:212634‑M2/141‑127 (MQ=255)                                                                                                                              tACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACCAATTATTAAGTAAt             >  2:52187/1‑141 (MQ=255)                                                                                                                              tACAAGGTTTCTACGTATCAAAACTGGGGGCAATATAAACGCGCTAATTTAAAAAGAAAAAAAACTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGAATTTGATAATGGTGCATCAGATAACTTATTaaaaaat             <  2:350890/141‑6 (MQ=255)                                                                                                                                         tATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAAAGa  >  1:150997/1‑141 (MQ=255)                                                                                                                                          |                                                                                                                                            ACATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAAAGA  >  USA300TCH1516_ALE/2128206‑2128482

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