New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	1417767 =	194 (0.950)	9 (0.050)	5/136	NT	5.9%	coding (152/831 nt)	gsiD_3	Glutathione transport system permease protein GsiD
	?	USA300TCH1516_ALE	1417824 =	121 (0.700)					coding (95/831 nt)	gsiD_3	Glutathione transport system permease protein GsiD

ATTTATTTTTGTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTTGCATTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/1417868‑1417767 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttggttgcatttTCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAATAAATGCAACGAATACAAAAAATATCAGGTTATTCTTTGAAAATATTT  >  USA300TCH1516_ALE/1417824‑1417911                                                                                                                                                                                                ATTTATTTTTGTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGT                                                                                                     <  2:1466129/91‑1    TATTTTTGTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGG                                                                                                  >  1:1625389/1‑91    TATTTTTGTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGG                                                                                                  >  1:1841521/1‑91     tagTTTGTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGT                                                                                                 <  2:3849492/88‑1     ATTTTTGTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCATCCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGT                                                                                                 <  2:3865974/91‑1     ATTTTTGTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGT                                                                                                 >  1:1019645/1‑91     ATTTTTGTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGT                                                                                                 >  1:3041642/1‑91     ATTTTTGTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGT                                                                                                 <  1:2325397/91‑1      TTTTTGTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTT                                                                                                >  1:1192499/1‑91      TTTTTGTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTT                                                                                                <  1:3251001/91‑1      TTTTTGTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTT                                                                                                <  1:3251132/91‑1      TTTTTGTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTT                                                                                                >  1:1192456/1‑91      TTTTTGTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTT                                                                                                >  1:685746/1‑91      TTTTTGTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTT                                                                                                >  1:2485348/1‑91      TTTTTGTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTT                                                                                                >  1:2485236/1‑91       TTTTGTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTTG                                                                                               <  2:2483483/91‑1       TTTTGTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTTG                                                                                               <  2:2483244/91‑1       TTTTGTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTTG                                                                                               <  1:831010/91‑1       TTTTGTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTTG                                                                                               <  2:3955277/91‑1        TTTGTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCACAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTTGC                                                                                              <  1:3416314/91‑1        TTTGTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTTGC                                                                                              >  1:625108/1‑91        TTTGTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTTGC                                                                                              <  2:580016/91‑1        TTTGTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTTGC                                                                                              <  1:1352415/91‑1         TTGTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTTGCA                                                                                             >  1:2253459/1‑91          TGTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTTGCAT                                                                                            <  2:1708834/91‑1          TGTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTTGCAT                                                                                            >  2:1414740/1‑91          TGTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTTGCAT                                                                                            <  2:1708651/91‑1          TGTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTTGCAT                                                                                            <  2:1708937/91‑1          TGTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTTGCAT                                                                                            >  1:2427952/1‑91           GTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTTGCATT                                                                                           <  2:993110/91‑1           GTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTTGCATT                                                                                           <  2:1093652/91‑1           GTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTTGCATT                                                                                           <  2:993019/91‑1           GTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTTGCATT                                                                                           <  1:393044/91‑1           GTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTTGCATT                                                                                           >  1:3839704/1‑91           GTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTTGCATT                                                                                           >  1:3839755/1‑91            TGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTTGCATTT                                                                                          <  2:2067645/91‑1            TGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTTGCATTT                                                                                          <  1:947527/91‑1                                             AAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTTGCATTTTCACTACTGACAAAGAATTGCAGTACAATTACC                                                         >  1:596189/1‑91                                                    AACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTTGCATTTTCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAA                                                  >  1:1322423/1‑91                                                    AACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTTGCATTTTCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAA                                                  >  1:2918760/1‑91                                                    AACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTTGCATTTTCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAA                                                  >  1:95483/1‑91                                                    AACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTTGCATTTTCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAA                                                  >  1:95572/1‑91                                                      CCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTTGCATTTTCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAATA                                                >  1:1051743/1‑91                                                       CAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTTGCATTTTCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAATAA                                               >  1:2920560/1‑91                                                       CAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTTGCATTTTCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAATAA                                               >  1:413151/1‑91                                                        AAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTTGCATTTTCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAATAAA                                              >  1:3236868/1‑91                                                                                           TTGGTTGCATTTTCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAATAAATGCAACGAATACAAAAAATATCAGGTTATTCTTTG           <  1:3400691/91‑1                                                                                           TTGGTTGCATTTTCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAATAAATGCAACGAATACAAAAAATATCAGGTTATTCTTTG           >  1:2319835/1‑91                                                                                           TTGGTTGCATTTTCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAATAAATGCAACGAATACAAAAAATATCAGGTTATTCTTTG           <  1:956119/91‑1                                                                                           TTGGTTGCATTTTCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAATAAATGCAACGAATACAAAAAATATCAGGTTATTCTTTG           >  2:1655778/1‑91                                                                                           TTGGTTGCATTTTCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAATAAATGCAACGAATACAAAAAATATCAGGTTATTCTTTG           <  1:3234064/91‑1                                                                                           TTGGTTGCATTTTCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAATAAATGAAAAAAAAAAAAAAAATATCAGGTTATTCTTTG           <  2:279173/91‑1                                                                                           TTGGTTGCATTTGCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAATAAATGCAACGAATACAAAAAATATCAGGTTATTCTTTG           <  2:1046426/91‑1                                                                                            TGGTTGCATTTTCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAATAAATGCAACGAATACAAAAAATATCAGGTTATTCTTTGA          <  2:1194894/91‑1                                                                                             GGTTGCATTTTCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAATAAATGCAACGAATACAAAAAATATCAGGTTATTCTTTGAA         <  1:1980529/91‑1                                                                                             GGTTGCATTTTCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAATAAATGCAACGAATACAAAAAATATCAGGTTATTCTTTGAA         <  1:3655625/91‑1                                                                                             GGTTGCATTTTCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAATAAATGCAACGAATACAAAAAATATCAGGTTATTCTTTGAA         >  1:2569232/1‑91                                                                                             GGTTGCATTTTCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAATAAATGCAACGAATACAAAAAATATCAGGTTATTCTTTGAA         <  1:3655679/91‑1                                                                                             GGTTGCATTTTCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAATAAATGCAACGAATACAAAAAATATCAGGTTATTCTTTGAA         >  1:2577693/1‑91                                                                                             GGTTGCATTTTCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAATAAATGCAACGAATACAAAAAATATCAGGTTATTCTTTGAA         <  2:2216888/91‑1                                                                                             GGTTGCATTTTCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAATAAATGCAACGAATACAAAAAATATCAGGTTATTCTTTGAA         >  1:2578888/1‑91                                                                                             GGTTGCATTTTCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAATAAATGCAACGAATACAAAAAATATCAGGTTATTCTTTGAA         <  2:2684076/91‑1                                                                                             GGTTGCATTTTCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAATAAATGCAAAAAATACAAAAAATATCAGGTTATTCTTTGAA         <  2:2684158/91‑1                                                                                              GTTGCATTTTCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAATAAATGCAACGAATACAAAAAATATCAGGTTATTCTTTGAAA        <  1:2791400/91‑1                                                                                               TTGCATTTTCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAATAAATGCAACGAATACAAAAAATATCAGGTTATTCTTTGAAAA       <  1:506101/91‑1                                                                                                 GCATTTTCACTACTGCCAAAGAATTGCAGTACACTTACCACAAAAATAAATGCAACGAATACAAAAAATATCAGGCTATTCTCTGAAAATA     >  2:186758/1‑91                                                                                                 GCATTTTCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAATAAATGCAACGAATACAAAAAATATCAGGTTATTCTTTGAAAATA     <  2:2083904/91‑1                                                                                                  CATTTTCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAATAAATGCAACGAATACAAAAAATATCAGGTTATTCTTTGAAAATAT    >  2:1430772/1‑91                                                                                                  CATTTTCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAATAAATGCAAAGAAAACAAAAAATATCAGGTTATTCTTTGAAAATAT    <  2:879813/91‑1                                                                                                  CATTTTCACTACTGACAAAGAATTGCAGTAAAATTACCACAAAAATAAATGCAACGAATACAAAAAATATCAGGTTATTCTTTGAAAATAT    <  2:879443/91‑1                                                                                                   ATTTTCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAATAAATGCAACGAATACAAAAAATATCAGGTTATTCTTTGAAAATATT   >  1:3190126/1‑91                                                                                                    TTTTCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAATAAATGCAACGAATACAAAAAATATCAGGTTATTCTTTGAAAATATTT  <  2:3366142/91‑1                                                                                                    TTTTCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAATAAATGCAACGAATACAAAAAATATCAGGTTATTCTTTGAAAATATTT  <  2:137493/91‑1                                                                                                    TTTTCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAATAAATGCAACGAATACAAAAAATATCAGGTTATTCTTTGAAAATATTT  <  2:439279/91‑1                                                                                                                                                                                                ATTTATTTTTGTGGTAATTGTACTGCAATTCTTTGTCAGTAGTGAAAATGCAACCAAAGTCAATTTATCACAAACTTTTGAACCTATTAGTTGGTTGCATTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/1417868‑1417767 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttggttgcatttTCACTACTGACAAAGAATTGCAGTACAATTACCACAAAAATAAATGCAACGAATACAAAAAATATCAGGTTATTCTTTGAAAATATTT  >  USA300TCH1516_ALE/1417824‑1417911

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ 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.