New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1353906	177 (0.870)	9 (0.050)	7/134	NT	5.6%	intergenic (+99/+44)	nucH/USA300HOU_RS06735	Thermonuclease/hypothetical protein
	?	USA300TCH1516_ALE	= 1353932	154 (0.900)					intergenic (+125/+18)	nucH/USA300HOU_RS06735	Thermonuclease/hypothetical protein

TAATTAAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1353805‑1353906 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaggcataataaTCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATCGATGCTTCAAGT  <  USA300TCH1516_ALE/1353932‑1353843                                                                                                                                                                                                  TAATTAAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAA                                                                                                       <  1:161087/91‑1  AATTAGATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAA                                                                                                      <  2:3208828/91‑1  AATTAAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAA                                                                                                      <  2:1128403/91‑1  AATTAAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAA                                                                                                      <  2:1128474/91‑1   ATTAAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAG                                                                                                     >  2:965719/1‑91   ATTAAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAG                                                                                                     >  1:1192359/1‑91   ATTAAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAG                                                                                                     <  2:1035299/91‑1    TTAAATAGGTGATTATATATATTAAAGTAAAATATGCTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGG                                                                                                    <  2:1967815/91‑1    TTAAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGG                                                                                                    >  2:89180/1‑91    TTAAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGG                                                                                                    <  1:3217755/91‑1    TTAAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTACTACCATAAATTTATATATAGAAATAATTTAAAGG                                                                                                    <  1:3242307/91‑1     TAAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGC                                                                                                   <  1:3485864/91‑1     TAAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGC                                                                                                   <  1:3485676/91‑1      AAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCA                                                                                                  >  1:737022/1‑91      AAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCA                                                                                                  >  1:1055189/1‑91      AAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCA                                                                                                  >  1:3724377/1‑91        ATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATA                                                                                                >  2:3083224/1‑91        ATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATA                                                                                                >  1:1413532/1‑91        ATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATA                                                                                                >  2:3331377/1‑91        ATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATA                                                                                                <  1:3801739/91‑1        ATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATA                                                                                                >  1:530715/1‑91         TAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAA                                                                                               >  1:3309367/1‑91         TAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAA                                                                                               >  1:3354635/1‑91         TAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAA                                                                                               <  2:81935/91‑1         TAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAA                                                                                               >  1:1907642/1‑91          AGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAAT                                                                                              <  2:1521725/91‑1          AGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAAT                                                                                              <  2:1521655/91‑1          AGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAAT                                                                                              <  2:1385837/91‑1           gggGATTATATATATTAAAGTAAAATATAATTGAAGCATAGATTTATTATTACCATAAATTTATATATAGAAATAATTTTAATGCATAATA                                                                                             >  2:1860745/4‑91           GGTGATTATATATATTAAAGTAAAATATACTTGAAGCCTCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATA                                                                                             >  1:3329642/1‑91           GGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATA                                                                                             <  1:2459523/91‑1           GGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATA                                                                                             <  2:450609/91‑1           GGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATA                                                                                             >  1:1565819/1‑91            GTGATTATATATATTAAAGTAAAATGTACTTGAAGCATCTATTTATTATTACCGTAAATTTATATATAGAAATAATTTAAAGGCATAATAA                                                                                            <  1:3669890/91‑1            GTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAA                                                                                            <  2:1315856/91‑1            GTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAA                                                                                            <  2:1113031/91‑1            GTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAA                                                                                            <  1:3840697/91‑1            GTGAGTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAA                                                                                            <  1:3296288/91‑1            GTGAGTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAA                                                                                            <  1:3296371/91‑1                                AAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAATCCATTACGCTCGATACGCA                                                                        <  2:2154139/91‑1                                AAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAAGAATTTAAAGGCATAATAATCCATTACGCTCGATACGCA                                                                        <  1:1157022/91‑1                                     ATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAATCCATTACGCTCGATACGCACTATG                                                                   <  1:3484320/91‑1                                       ACTTGACGCATCGATTTATTACTACCATAGATTTATATATAGAAGTAATTTAAAGGCATAATAATCCATTACGCTCGATACGCACTATGGT                                                                 <  2:2209130/91‑1                                          TGAATCATCGATTTATTATTTCCAGATATTTATATATAGAAATAATTTAAAATCATAATAATCCATTACGCTCGATACGCACTATGGTTAT                                                              <  2:2559410/91‑1                                          TGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAATCCATTACGCTCGATACGCACTATGGTTAT                                                              <  2:1994602/91‑1                                           GAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAATCCATTACGCTCGATACGCACTATGGTTATT                                                             <  2:3234161/91‑1                                              GCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAATCCATTACGCTCGATACGCACTATGGTTATTATG                                                          <  2:3613936/91‑1                                                  CGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAATCCATTACGCTCGATACGCACTATGGTTATTATGCCTT                                                      <  2:933354/91‑1                                                                                          AAAGGCATAATAATCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATC              >  2:1129421/1‑91                                                                                          AAAGGCATAATAATCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATCTCTATATATAAATTTATGGTAATAATAAATC              >  2:1128679/1‑91                                                                                           AAGGCATAATAATCCATTATGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATCG             >  2:1802549/1‑91                                                                                           AAGGCATAATAATCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATCG             >  2:2599180/1‑91                                                                                           AAGGCATAATAATCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATCG             <  1:1582317/91‑1                                                                                           AAGGCATAATAATCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATCG             >  2:419000/1‑91                                                                                            AGGCATAATAATCCATTACGCTCGATACGCCCTATTGTTACTATGCCTTTACCTCTTTCCTATATATAAATTTATGGTAATAATAAATCGA            >  2:1972961/1‑91                                                                                            AGGCATAATAATCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATCGA            >  2:2044826/1‑91                                                                                            AGGCATAATAATCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATCGA            <  1:3074543/91‑1                                                                                            AGGCATAATAATCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATCGA            >  2:3803149/1‑91                                                                                            AGGCATAATAATCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATCGA            <  2:658990/91‑1                                                                                            AGGCATAATAATCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTGATGGTAATAATAAATCGA            >  1:2826789/1‑91                                                                                             GGCATAATAATCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATCGAT           <  1:943460/91‑1                                                                                              GCATAATAATCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATCGATc          >  2:3096782/1‑90                                                                                              GCATAATAATCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATCGATG          >  1:1964579/1‑91                                                                                              GCATAATAATCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATCGATG          >  2:3096766/1‑91                                                                                              GCATAATAATCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATCGATG          >  2:3683065/1‑91                                                                                              GCATAATAATCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATCGATG          >  1:3419139/1‑91                                                                                               CATAATAATCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATCGATGC         <  2:1159958/91‑1                                                                                               CATAATAATCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATCGATGC         <  1:1812637/91‑1                                                                                                ATAATAATCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATCGATGCT        >  1:3840330/1‑91                                                                                                 TAATAATCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATCGATGCTT       >  2:1144075/1‑91                                                                                                  AATAATCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATCGATGCTTC      <  1:617595/91‑1                                                                                                   ATAATCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATCGATGCTTCA     <  1:633782/91‑1                                                                                                   ATAATCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATCGATGCTTCA     <  1:1126799/91‑1                                                                                                   ATAATCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATCGATGCTTCA     <  1:633627/91‑1                                                                                                    TAATCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATCGATGCTTCAA    >  2:2117618/1‑91                                                                                                     AATCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATCGATGCTTCAAG   <  1:1564099/91‑1                                                                                                     AATCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATCGATGCTTCAAG   <  1:1367216/91‑1                                                                                                     AATCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATCGATGCTTCAAG   >  2:1965367/1‑91                                                                                                      ATCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATCGATGCTCCAAGT  >  2:3198323/1‑91                                                                                                                                                                                                  TAATTAAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1353805‑1353906 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaggcataataaTCCATTACGCTCGATACGCACTATGGTTATTATGCCTTTAAATTATTTCTATATATAAATTTATGGTAATAATAAATCGATGCTTCAAGT  <  USA300TCH1516_ALE/1353932‑1353843

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.