New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 365040	123 (0.600)	23 (0.130)	10/136	NT	16.0%	intergenic (+50/+55)	nupC_1/sglT	Nucleoside permease NupC/Sodium/glucose cotransporter
	?	USA300TCH1516_ALE	= 365070	138 (0.800)					intergenic (+80/+25)	nupC_1/sglT	Nucleoside permease NupC/Sodium/glucose cotransporter

TTCAACTCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCAC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/364939‑365040 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaccccgtcacTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTTACAATACT  <  USA300TCH1516_ALE/365070‑364981                                                                                                                                                                                                  TTCAACTCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTA                                                                                                       >  1:2706107/1‑91 TTCAACTCTAGCTTCAAGCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCAGGGCAAAGCTA                                                                                                       <  2:1859702/91‑1  TCAACTCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCGAAGCTAA                                                                                                      >  1:1956080/1‑91  TCAACTCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAA                                                                                                      <  2:2267485/91‑1   CAACTCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTCGTATCGTAAATGCAACGAAGTACCTACATTAAATTCATGGCAAAGCTCAA                                                                                                     >  2:169493/1‑91   CAACTCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAA                                                                                                     <  2:148531/91‑1   CAACTCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAA                                                                                                     >  2:2758567/1‑91   CAACTCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAA                                                                                                     >  1:1231538/1‑91   CAACTCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCCAAGTACCTAAATTAAATTCATGGCAAAGCTAAA                                                                                                     >  1:3239731/1‑91    AACTCTAGCTTCAATCATTTCAGGATCAATTATTGGCTTAGTATTGTAAATTAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAAC                                                                                                    >  2:3895935/1‑91    AACTCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAAC                                                                                                    >  2:1804105/1‑91    AACTCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAAC                                                                                                    >  2:2794063/1‑91    AACTCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAAC                                                                                                    >  2:2794019/1‑91     ACTCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACC                                                                                                   >  1:3018561/1‑91      CTCTAGCTTCAATTATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAATTTCATGGCTAAGCTAATCCC                                                                                                  >  2:2802794/1‑91      CTCTAGCTTCAATTATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCC                                                                                                  >  2:2804952/1‑91      CTCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCC                                                                                                  <  1:2438133/91‑1      CTCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCC                                                                                                  >  2:188785/1‑91       TCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCC                                                                                                 >  1:902889/1‑91        CTAGCTTCAATCCTTTCAGCATCAATCTTTGGCTTAGTATAGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCG                                                                                                <  2:895205/91‑1        CTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCG                                                                                                >  2:2224792/1‑91        CTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCG                                                                                                <  2:1661863/91‑1         TAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGT                                                                                               >  1:2317160/1‑91         TAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGT                                                                                               <  2:138610/91‑1          AGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTC                                                                                              >  1:734926/1‑91          AGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTC                                                                                              >  2:90224/1‑91          AGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTC                                                                                              >  1:1727728/1‑91           GCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCA                                                                                             <  1:1117118/91‑1            CTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCAC                                                                                            <  2:1701/91‑1            CTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCAC                                                                                            <  2:3862674/91‑1            CTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCAC                                                                                            <  1:2589452/91‑1                           GATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGC                                                                             <  1:1813991/91‑1                           GATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGC                                                                             <  1:1827889/91‑1                                   ATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGCTGTTGCGC                                                                     <  1:2024670/91‑1                                       GCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAAC                                                                 <  1:3077986/91‑1                                       GCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAAC                                                                 <  1:3649699/91‑1                                       GCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAAC                                                                 <  2:2004673/91‑1                                       GCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAAC                                                                 <  1:3077987/91‑1                                        CTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACT                                                                <  1:1732329/91‑1                                        CTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACT                                                                <  2:2501368/91‑1                                         gTAGTATTGTAAATGAATCGAAGTACCTAAATTAAAGTCATGGCAAAGCTAAACCCCGTCACTAAGTGATGATGCGCTGTTGCGCCAACTT                                                               <  2:3917942/90‑1                                         TTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTT                                                               <  1:2560179/91‑1                                         TTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTT                                                               <  1:866555/91‑1                                         TTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTT                                                               <  1:1323833/91‑1                                         TTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTT                                                               <  2:3850679/91‑1                                         TTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTT                                                               <  2:3533992/91‑1                                          TAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTG                                                              <  2:2316883/91‑1                                          TAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTG                                                              <  1:2255272/91‑1                                          TAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTG                                                              <  1:642266/91‑1                                          TAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTG                                                              <  1:642050/91‑1                                              ATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGA                                                          <  1:2883438/91‑1                                               TTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGAC                                                         <  1:1135441/91‑1                                                TGTAAATGAATCGAAGTACCTAAATTAAGTTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACG                                                        <  2:3041883/91‑1                                                 GTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGG                                                       <  1:476335/91‑1                                                                                           AAACCCCGTTACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCA             <  1:3795173/91‑1                                                                                           AAACCCCGTGACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCA             <  1:3794363/91‑1                                                                                           AAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCA             <  2:2135322/91‑1                                                                                           AAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCA             <  2:3710979/91‑1                                                                                           AAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCA             <  2:3710811/91‑1                                                                                            AACCCCGTCTCTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCct            >  2:541107/1‑89                                                                                              CCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTT          >  2:3225696/1‑91                                                                                              CCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTT          >  1:2050774/1‑91                                                                                              CCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTT          >  1:2051288/1‑91                                                                                              CCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTT          >  2:3225668/1‑91                                                                                               CCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTTA         >  1:303145/1‑91                                                                                                CCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTTAC        >  2:3910523/1‑91                                                                                                 CGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTGGATTCATTTACA       <  1:3050265/91‑1                                                                                                 CGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTTACA       >  1:3015368/1‑91                                                                                                 CGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTTACA       >  1:1791415/1‑91                                                                                                  GTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGCAATTAATTTAGGTACTTCGATTCATTTACAA      >  1:3165613/1‑91                                                                                                   TCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTTACAAT     >  1:1853382/1‑91                                                                                                    CACTAAGTTATGATGCGCTGTTGCGCCAACTTGCTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTCACAATA    >  2:556211/1‑91                                                                                                     ACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCTATTCATTTACAATAC   <  2:994627/91‑1                                                                                                     ACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCTATTCATTTACAATAC   <  2:993961/91‑1                                                                                                     ACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTTACAATAC   <  1:1706543/91‑1                                                                                                      CTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCTTTTACAATACT  >  1:718569/1‑91                                                                                                      CTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTTACAATACT  <  2:2441157/91‑1                                                                                                      CTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTTACAATACT  <  2:2441118/91‑1                                                                                                                                                                                                  TTCAACTCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCAC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/364939‑365040 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaccccgtcacTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTTACAATACT  <  USA300TCH1516_ALE/365070‑364981

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.