New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2014149	193 (1.010)	15 (0.090)	11/148	NT	7.5%	intergenic (+49/+212)	USA300HOU_RS10140/USA300HOU_RS10150	hypothetical protein/hypothetical protein
	?	USA300TCH1516_ALE	= 2014182	192 (1.090)					intergenic (+82/+179)	USA300HOU_RS10140/USA300HOU_RS10150	hypothetical protein/hypothetical protein

GGGTATTTACAGAAGATAAGTTACAACGTAAACTGTATGCTAAATAATTTCAAGTTATTATTCACTAAAGTTAATCTATAAAAAATGAACAACCGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2014054‑2014149 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaccggACAGAGTAAAAATCGTTTTGATTTTCATTCTGCCCGGTTGTTCATTTTTTATAGATTAACTTTAGTGAATAATAACTTGAAATTATTTAG  <  USA300TCH1516_ALE/2014182‑2014093                                                                                                                                                                                            GGGTATTTACAGAAGATAAGTTACAACGTAAACTGTATGCTAAATAATTTCAAGTTATTATTCACTAAAGTTAATCTATAAAAAATGAACA                                                                                                 >  2:2748468/1‑91  GGTATTTACAGAAGATAAGTTACAACGTAAACTGTATGCTAAATAATTTCAAGTTATTATTCACTAAAGTTAATCTATAAAAAATGAACAA                                                                                                <  2:3107328/91‑1  GGTATTTACAGAAGATAAGTTACAACGTAAACTGTATGCTAAATAATTTCAAGTTATTATTCACTAAAGTTAATCTATAAAAAATGAACAA                                                                                                <  1:3860008/91‑1  GGTATTTACAGAAGATAAGTTACAACGTAAACTGTATGCTAAATAATTTCAAGTTATTATTCACTAAAGTTAATCTATAAAAAATGAACAA                                                                                                <  1:1907934/91‑1  GGTATTTACAGAAGATAAGTTACAACGTAAACTGTATGCTAAATAATTTCAAGTTATTATTCACTAAAGTTAATCTATAAAAAATGAACAA                                                                                                <  2:1279328/91‑1   GTATTTACAGAAGATAAGTTACAACGTAAACTGTATGCTAAATAATTTCAAGTTATTATTCACTAAAGTTAATCTATAAAAAATGAACAAC                                                                                               >  2:1584820/1‑91   GTATTTACAGAAGATAAGTTACAACGTAAACTGTATGCTAAATAATTTCAAGTTATTATTCACTAAAGTTAATCTATAAAAAATGAACAAC                                                                                               >  1:2782243/1‑91   GTATTTACAGAAGATAAGTTACAACGTAAACTGTATGCTAAATAATTCCTAGTTATTATTCACTAAAGTTAATCTATAAAAAATGAACAAC                                                                                               >  2:805023/1‑91    TATTTACAGAAGATAAGTTACAACGTAAACTGTATGCTAAATAATTTCAAGTTATTATTCACTAAAGTTAATCTATAAAAAATGAACAACC                                                                                              >  1:857529/1‑91    TATTTACAGAAGATAAGTTACAACGTAAACTGTATGCTAAATAATTTCAAGTTATTATTCACTAAAGTTAATCTATAAAAAATGAACAACC                                                                                              >  1:857123/1‑91    TATTTACAGAAGATAAGTTACAACGTAAACTGTATGCTAAATAATTACAAGTTATTATTCACTAGAGTTAAACTATAAAAAATGAACAACC                                                                                              >  2:2232150/1‑91     ATTTACAGAAGATAAGTTACAACGTAAACTGTATGCTAAATAATTTCAAGTTATTATTCACTAAAGTTAATCTATAAAAAATGAACAACCG                                                                                             <  1:683145/91‑1     ATTTACAGAAGATAAGTTACAACGTAAACTGTATGCTAAATAATTTCAAGTTATTATTCACTAAAGTTAATCTATAAAAAATGAACAACCG                                                                                             >  2:1113591/1‑91         ACAGAAGATAAGTTACAACGTAAACTGTATGCTAAATAATTTCAAGTTATTATTCACTAAAGTTAATCTATAAAAAATGAACAACCG                                                                                             >  1:3707571/1‑87         ACAGAAGATAAGGTACAACGTAAACTGTATGCTAAATAATTTCAAGTTATTATTCACTAAAGTTAATCTATAAAAAATGAACAACCG                                                                                             <  2:3707571/87‑1                         AACGTAAACTGTATGCTAAATAATTTCAAGTTATTATTCACTAAAGTTAATCTATAAAAAATGAACAATCGGACAGAGTAAAAATCGTTTg                                                                         <  2:809966/91‑2                          ACGTAAACTGTGTGCTAAATAATTTCAAGTTATTATTCACTAAAGTTAATCTATAAAAAATGAACAACCGGACAGAGTAAAAATCGTTTTG                                                                        <  1:3514262/91‑1                                    TATGCTAAATAATTTCAAGTTATTATTCACTAAAGTTAATCTATAAAAAATGAACAACCGGACAGAGTAAAAATCGTTTTGATTTTCATTC                                                              <  1:3415555/91‑1                                    TATGCTAAATAATTTCAAGTTATTATTCACTAAAGTTAATCTATAAAAAATGAACAACCGGACAGAGTAAAAATCGTTTTGATTTTCATTC                                                              <  2:528788/91‑1                                      TGCTAAATAATTTCAAGTTATTATTCACTAAAGTTAATCTATAAAAAATGCACAACCGGACAGAGTAAAAATCGTTTTGATTTTCATTCTG                                                            <  2:3186664/91‑1                                        CTAAATAATTTCAAGTTATTATTCACTAAAGTTAATCTATAAAAAATGAACAACCGGACAGAGTAAAAATCGTTTTGATTTTCATTCTGCC                                                          <  2:89892/91‑1                                         TAAATAATTTCAAGTTATTATTCACTAAAGTTAATCTATAAAAAATGAACAACCGGACAGAGTAAAAATCGTTTTGATTTTCATTCTGCCC                                                         <  2:573198/91‑1                                         TAAATAATTTCAAGTTATTATTCACTAAAGTTAATCTATAAAAAATGAACAACCGGACAGAGTAAAAATCGTTTTGATTTTCATTCTGCCC                                                         <  1:2331356/91‑1                                         TAAATAATTTCAAGTTATTATTCACTAAAGTTAATCTATAAAAAATGAACAACCGGACAGAGTAAAAATCGTTTTGATTTTCATTCTGCCC                                                         <  1:1177124/91‑1                                           AATAATTTCAAGTTATTATTCACTAAAGTTAATCTATAAAAAATGAACAACCGGACAGAGTAAAAATCGTTTTGATTTTCATTCTGCCCGG                                                       <  1:1658635/91‑1                                            ATAATTTCAAGTTATTATTCACTAAAGTTAATCTATAAAAAATGAACAACCGGACAGAGTAAAAATCGTTTTGATTTTCATTCTGCCCGGT                                                      <  1:1345221/91‑1                                             TAATTTCAAGTTATTATTCACTAAAGTTAATCTATAAAAAATGAACAACCGGACAGAGTAAAAATCGTTTTGATTTTCATTCTGCCCGGTT                                                     <  2:2868477/91‑1                                              AATTTCAAGTTATTATTCACTAAAGTTAATCTATAAAAAATGAACAACCGGACAGAGTAAAAATCGTTTTGATTTTCATTCTGCCCGGTTG                                                    <  1:2911706/91‑1                                                TTTCAAGTTATTATTCACTAAAGTTAATCTATAAAAAATGAACAACCGGACAGAGTAAAAATCGTTTTGATTTTCATTCTGCCCGGTTGTT                                                  <  2:2019943/91‑1                                                       TTATTATTCACTAAAGTTAATCTATAAAAAATGAACAACCGGACAGAGTAAAAATCGTTTTGATTTTCATTCTGCCCGGTTGTTCATTTTT                                           <  1:2698212/91‑1                                                                                       GAACAACCGGACAGAGTAAAAATCGTTTTGATTTTCATTCTGCCCGGTTGTTCATTTTTTATAGATTAACTTTAGTGAATAATAACTTGAA           <  1:427805/91‑1                                                                                           AACCGGACAGAGTAAAAATCGTTTTGATTTTCATTCTGCCCGGTTGTTCATTTTTTATAGATTCACTTTAGTGAATAATAACTTGAAATTt       >  2:3518029/1‑90                                                                                           AACCGGACAGAGTAAAAATCGTTTTGATTTTCATTCTGCCCGGTTGTTCATTTTTTATAGATTAACTTTAGTGAATAATAACTTGAAATTA       >  2:759522/1‑91                                                                                             CCGGACAGAGTAAAAATCGTTTTGATTTTCATTCTGCCCGGTTGTTCATTTTTTATAGATTACCTTTAGTGAATAATAACTTGAAATTATT     >  2:1480953/1‑91                                                                                             CCGGACAGAGTAAAAATCGTTTTGATTTTCATTCTGCCCGGTTGTTCATTTTTTATAGATTAACTTTAGTGAATAATAACTTGAAATTATT     >  2:367340/1‑91                                                                                             CCGGACAGAGTAAAAATCGTTTTGATTTTCATTCTGCCCGGTTGTTCATTTTTTATAGATTAACTTTAGTGAATAATAACTTGAAATTATT     >  2:99272/1‑91                                                                                             CCGGACAGAGTAAAAATCGTTTTGATTTTCATTCTGCCCGGTTGTTCATTTTTTATAGATTAACTTTAGTGAATAATAACTTGAAATTATT     >  1:2673152/1‑91                                                                                             CCGGACAGAGTAAAAATCGTTTTGATTTTCATTCTGCCCGGTTGTTCATTTTTTATAGATTAACTTTAGTGAATAATAACTTGAAATTATT     >  1:2684404/1‑91                                                                                             CCGGACAGAGTAAAAATCGTTTTGATTTTCATTCTGCCCGGTTGTTCATTTTTTATAGATTAACTTTAGTGAATAATAACTTGAAATTATT     >  2:2061959/1‑91                                                                                              CGGACAGAGTAAAAATCGTTTTGATTTTCATTCTGCCCGGTTGTTCATTTTTTATAGATTAACTTTAGTGAATAATAACTTGAAATTATTT    <  1:2764699/91‑1                                                                                              CGGACAGAGTAAAAATCGTTTTGATTTTCATTCTGCCCGGTTGTTCATTTTTTATAGATTAACTTTAGTGAATAATAACTTGAAATTATTT    >  2:2647559/1‑91                                                                                              CGGACAGAGTAAAAATCGTTTTGATTTTCATTCTGCCCGGTTGTTCATTTTTTATAGATTAACTTTAGTGAATAATAACTTGAAATTATTT    <  1:1913142/91‑1                                                                                               GGACAGAGTAAAAATCGTTTTGATTTTCATTCTGCCCGGTTGTTCATTTTTTATAGATTAACTTTAGTGAATAATAACTTGAAATTATTTA   >  1:2799326/1‑91                                                                                                GACAGAGTAAAAATCGTTTTGATTTTCATTCTGCCCGGTTGTTCATTTTTTATAGATTAACTTTAGTGAATAATAACTTGAAATTATTTAG  >  1:666736/1‑91                                                                                                GACAGAGTAAAAATCGTTTTGATTTTCATTCTGCCCGGTTGTTCATTTTTTATAGATTAACTTTAGTGAATAATAACTTGAAATTATTTAG  >  2:2168470/1‑91                                                                                                GACAGAGTAAAAATCGTTTTGATTTTCATTCTGCCCGGGTGTTCATTTTTTATAGATTAACTTTAGTGAATAATAACTTGAAATTATTTAG  >  2:3716407/1‑91                                                                                                                                                                                            GGGTATTTACAGAAGATAAGTTACAACGTAAACTGTATGCTAAATAATTTCAAGTTATTATTCACTAAAGTTAATCTATAAAAAATGAACAACCGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2014054‑2014149 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaccggACAGAGTAAAAATCGTTTTGATTTTCATTCTGCCCGGTTGTTCATTTTTTATAGATTAACTTTAGTGAATAATAACTTGAAATTATTTAG  <  USA300TCH1516_ALE/2014182‑2014093

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.