New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	1205038 =	91 (0.930)	16 (0.180)	11/148	NT	16.0%	coding (82/195 nt)	USA300HOU_RS15290	hypothetical protein
	?	USA300TCH1516_ALE	= 1427022	NA (NA)					intergenic (‑753/+219)	pstS/cvfB	Phosphate‑binding protein PstS/Conserved virulence factor B

CTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTT  >  USA300TCH1516_ALE/1426974‑1427111                                                 |                                                                                          cTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTcc                                                 >  1:876641/1‑91 (MQ=31)  tAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCa                                                <  1:276736/91‑1 (MQ=32)   aGGTTTTGTATTAATGGCACTTAATATAAGGATAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCAt                                               <  1:3527185/91‑1 (MQ=18)   aGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCAt                                               >  1:293709/1‑91 (MQ=33)     gTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCa                                             <  1:671535/91‑1 (MQ=34)     gTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCa                                             >  1:322356/1‑91 (MQ=33)      ttttGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCaa                                            <  1:3584592/91‑1 (MQ=33)      ttttGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCaa                                            >  1:1441039/1‑91 (MQ=34)          gTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAaataa                                        <  1:2461410/91‑1 (MQ=34)           tATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAaataat                                       >  1:3130251/1‑91 (MQ=34)           tATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAaataat                                       >  1:353643/1‑91 (MQ=33)            aTTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAAtaatt                                      >  1:3435201/1‑91 (MQ=33)              tAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAAtaattaa                                    <  1:1546294/91‑1 (MQ=34)               aaTGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAAtaattaat                                   <  1:1938513/91‑1 (MQ=34)               aaTGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAAtaattaat                                   >  1:2854897/1‑91 (MQ=34)                   gCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGaa                               <  1:3083579/91‑1 (MQ=34)                   gCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGaa                               >  1:4054370/1‑91 (MQ=34)                   gCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGaa                               <  1:3083545/91‑1 (MQ=33)                     aCTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAAt                             <  1:1144637/91‑1 (MQ=34)                      cTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATc                            <  1:1413835/91‑1 (MQ=34)                       ttAGTATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAACTAATAGAAATCa                           <  1:3209416/91‑1 (MQ=255)                       ttAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCa                           >  1:2653685/1‑91 (MQ=34)                       ttAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCa                           <  1:1791965/91‑1 (MQ=34)                        tAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAg                          <  1:2419445/91‑1 (MQ=34)                        tAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAg                          <  1:3316574/91‑1 (MQ=34)                        tAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAg                          <  1:2702037/91‑1 (MQ=34)                        tAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAg                          <  1:2702036/91‑1 (MQ=34)                        tAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAg                          >  1:4135404/1‑91 (MQ=33)                        tAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAg                          <  1:2419729/91‑1 (MQ=34)                        tAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAg                          <  1:2419682/91‑1 (MQ=34)                         aaTATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGc                         >  1:3349374/1‑91 (MQ=33)                         aaTATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGc                         >  1:3349246/1‑91 (MQ=33)                           tataAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCtt                       >  1:577339/1‑91 (MQ=34)                           tataAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCtt                       <  1:358087/91‑1 (MQ=34)                             taAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCtttt                     <  1:1263226/91‑1 (MQ=34)                             taAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCtttt                     <  1:2688967/91‑1 (MQ=33)                                  aaaaTAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACa                >  1:2971258/1‑91 (MQ=34)                                  aaaaTAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACa                >  1:1290717/1‑91 (MQ=34)                                  aaaaTAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACa                >  1:436021/1‑91 (MQ=33)                                    aaTAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACAtt              >  1:2891610/1‑91 (MQ=33)                                       agcagcTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGcc           >  1:3380493/1‑91 (MQ=34)                                        gcagcTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCt          >  1:3558882/1‑91 (MQ=34)                                         cagcTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTa         >  1:1197976/1‑91 (MQ=34)                                          agcTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTaa        <  1:1405903/91‑1 (MQ=34)                                           gcTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAg       >  1:3289083/1‑91 (MQ=33)                                            cTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGa      <  1:4045124/91‑1 (MQ=34)                                            cTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGa      <  1:3833739/91‑1 (MQ=34)                                               aaCGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACt   <  1:3922254/91‑1 (MQ=34)                                               aaCGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACt   <  1:145687/91‑1 (MQ=33)                                               aaCGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAAGCAGCTTTTTTACATTGCCTAAGAACt   <  1:3924036/91‑1 (MQ=21)                                                aCGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACtt  <  1:574574/91‑1 (MQ=34)                                                aCGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACtt  <  1:574590/91‑1 (MQ=34)                                                 |                                                                                          CTAGGTTTTGTATTAATGGCACTTAATATAAGGAAAATAGCAGCTCAACGAGCTGTACATTATAAAATACATATCAAAAAAGCTGATTTCCATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAACTT  >  USA300TCH1516_ALE/1426974‑1427111

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