New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 365040	144 (0.760)	15 (0.090)	11/136	NT	10.7%	intergenic (+50/+55)	nupC_1/sglT	Nucleoside permease NupC/Sodium/glucose cotransporter
	?	USA300TCH1516_ALE	= 365070	128 (0.790)					intergenic (+80/+25)	nupC_1/sglT	Nucleoside permease NupC/Sodium/glucose cotransporter

TTCAACTCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCAC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/364939‑365040 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaccccgtcacTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTTACAATAC  <  USA300TCH1516_ALE/365070‑364982                                                                                                                                                                                                 TTCAACTCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTA                                                                                                      >  1:2019843/1‑91 TTCAACTCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTA                                                                                                      >  1:2672165/1‑91  TCAACTCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAA                                                                                                     <  1:2156420/91‑1   CAACTCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAA                                                                                                    <  1:3820506/91‑1    AACTCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAAC                                                                                                   >  2:2214915/1‑91    AACTCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAAC                                                                                                   >  1:2190950/1‑91    AACTCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAAC                                                                                                   >  1:2192484/1‑91     ACTCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACC                                                                                                  <  1:3550458/91‑1     ACTCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACC                                                                                                  <  1:3550395/91‑1     ACTCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACC                                                                                                  >  1:362862/1‑91     ACTCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACC                                                                                                  >  1:1433537/1‑91     ACTCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACC                                                                                                  >  1:1271913/1‑91      CTCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAACTTCATGGCAAAGCTCAACCC                                                                                                 >  1:1418260/1‑91      CTCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCC                                                                                                 >  2:2628474/1‑91      CTCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCC                                                                                                 >  1:1418267/1‑91       TCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCC                                                                                                <  1:2905427/91‑1       TCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCC                                                                                                <  1:252331/91‑1        CTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCG                                                                                               <  2:783410/91‑1        CTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCG                                                                                               >  2:2079992/1‑91        CTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCG                                                                                               >  1:3380823/1‑91        CTAGCTTCAATCATTTCAGGACCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCG                                                                                               >  1:2535320/1‑91         TAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGT                                                                                              >  1:26470/1‑91          AGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTC                                                                                             <  2:929452/91‑1          AGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTC                                                                                             <  1:3818533/91‑1          AGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTC                                                                                             <  1:53240/91‑1          AGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTC                                                                                             <  1:1377253/91‑1          AGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAAC                                                                                                   <  2:2144627/85‑1          AGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAAC                                                                                                   >  1:2144627/1‑85           GCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCA                                                                                            <  1:2198384/91‑1           GCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCA                                                                                            >  1:2628521/1‑91           GCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCA                                                                                            >  1:1512167/1‑91           GCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCA                                                                                            >  1:1512422/1‑91            CTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCAC                                                                                           <  2:1071701/91‑1            CTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCAC                                                                                           <  1:149645/91‑1            CTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCAC                                                                                           <  2:1362570/91‑1                        CAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCC                                                                                                >  2:1464185/1‑74                        CAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCC                                                                                                <  1:1464185/74‑1                              CAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCACCAAGTTATGATGCGCTGT                                                                         <  2:2198441/91‑1                                  CATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGCTGTTGCG                                                                     <  2:1374504/91‑1                                  CATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGCTGTTGCG                                                                     >  2:904011/1‑91                                    TTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCC                                                                   <  1:3650695/91‑1                                       GCTTAGTATTGTAAATGAATCGAAGTACCTAAATTACATTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAAC                                                                <  2:3830229/91‑1                                       GCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAAC                                                                <  2:3385928/91‑1                                         TTAGTATTGTAAATGAATCGAAGTGCCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTT                                                              <  1:2795811/91‑1                                         TTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTT                                                              <  2:2646964/91‑1                                         TTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTT                                                              <  2:1356291/91‑1                                          TAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTG                                                             <  1:1144134/91‑1                                          TAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTG                                                             <  1:1122436/91‑1                                           AGTACTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGG                                                            <  1:3234834/91‑1                                                TGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACG                                                       <  2:2248627/91‑1                                                             AAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTG                                          <  1:904011/91‑1                                                                TACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCA                                       <  1:67761/91‑1                                                                                           tAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCTACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCA            <  2:3843144/90‑1                                                                                           AAACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCA            <  1:2423663/91‑1                                                                                            AACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTAGATTCAT           >  1:1939419/1‑91                                                                                             ACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATT          <  1:848059/91‑1                                                                                             ACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATT          >  1:2371349/1‑91                                                                                             ACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATT          <  1:1769589/91‑1                                                                                             ACCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATT          >  1:2371388/1‑91                                                                                              CCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTT         >  1:861128/1‑91                                                                                              CCCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTT         >  1:1412189/1‑91                                                                                               CCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTTA        <  1:3820562/91‑1                                                                                               CCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTTA        <  2:3293018/91‑1                                                                                               CCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTTA        <  1:2219986/91‑1                                                                                               CCCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTTA        <  2:2673085/91‑1                                                                                                CCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTGGCTTTGCCATGAATTTACTTTAGGTACTTCGATTCGTTTAC       >  2:3576737/1‑91                                                                                                CCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTTAC       >  2:3691067/1‑91                                                                                                CCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTTAC       <  1:1843713/91‑1                                                                                                CCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTTAC       >  2:3691010/1‑91                                                                                                CCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTTAC       <  2:948698/91‑1                                                                                                CCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTTAC       >  2:2706003/1‑91                                                                                                CCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTTAC       >  2:2706002/1‑91                                                                                                CCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTTAC       >  2:2326876/1‑91                                                                                                CCGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTTAC       >  2:1568008/1‑91                                                                                                CCGTCACGAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATATAATTTAGGTACTTCGATTCATTTAC       <  2:2224963/91‑1                                                                                                 CGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTTACA      >  2:2560720/1‑91                                                                                                 CGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTTACA      >  1:1861661/1‑91                                                                                                 CGTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTTACA      >  2:1015736/1‑91                                                                                                  GTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTTACAA     <  2:3215500/91‑1                                                                                                  GTCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTTACAA     >  2:2195108/1‑91                                                                                                   TCACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTTACAAT    >  1:2893988/1‑91                                                                                                    CACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTTGCAATA   >  2:3573599/1‑91                                                                                                    CACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTTACAATA   <  1:3482246/91‑1                                                                                                     ACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCGTGAATTTAATTTAGGTACTTCGATTCATTTACAATAC  <  1:3271695/91‑1                                                                                                     ACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCGTGAATTTAATTTAGGTACTTCGATTCATTTACAATAC  <  1:972344/91‑1                                                                                                     ACTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTTACAATAC  <  2:3234361/91‑1                                                                                                                                                                                                 TTCAACTCTAGCTTCAATCATTTCAGGATCAATCATTGGCTTAGTATTGTAAATGAATCGAAGTACCTAAATTAAATTCATGGCAAAGCTAAACCCCGTCAC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/364939‑365040 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaccccgtcacTAAGTTATGATGCGCTGTTGCGCCAACTTGGTGACGGGGTTTAGCTTTGCCATGAATTTAATTTAGGTACTTCGATTCATTTACAATAC  <  USA300TCH1516_ALE/365070‑364982

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.