New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	1181842 =	245 (0.850)	13 (0.050)	8/144	NT	6.1%	intergenic (+409/+65)	USA300HOU_RS05885/USA300TCH1516_01103	hypothetical protein/tRNA‑Arg
	?	USA300TCH1516_ALE	1181881 =	178 (0.690)					intergenic (+448/+26)	USA300HOU_RS05885/USA300TCH1516_01103	hypothetical protein/tRNA‑Arg

ATCGGTCGGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTTTTTGTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/1181939‑1181842 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttttgtttGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTCGAACCCCCGACCGATGGCTTAGAAGGCCATTGCTCTATCCAGCTGA  >  USA300TCH1516_ALE/1181881‑1181970                                                                                                                                                                                              ATCGGTCGGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTT                                                                                                   <  1:543651/91‑1 ATCGGTCGGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTT                                                                                                   >  2:1776875/1‑91  TCGGTCGGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTTT                                                                                                  <  2:70948/91‑1  TCGGTCGGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTTT                                                                                                  <  2:4688638/91‑1  TCGGTCGGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTTT                                                                                                  <  2:4095559/91‑1  TCGGTCGGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTTT                                                                                                  <  2:4095358/91‑1  TCGGTCGGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTTT                                                                                                  <  1:4037394/91‑1  TCGGTCGGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTTT                                                                                                  <  2:3232566/91‑1  TCGGTCGAGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTTT                                                                                                  <  1:4089630/91‑1   CGGTCGGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTTTT                                                                                                 <  1:71755/91‑1   CGGTCGGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTTTT                                                                                                 <  2:1316771/91‑1   CGGTCGGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTTTT                                                                                                 <  2:1316659/91‑1   CGGTCGGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTTTT                                                                                                 <  1:2839739/91‑1   CGGTCGGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTTTT                                                                                                 >  2:3839739/1‑91   CGGTCGGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTTTT                                                                                                 >  1:1042026/1‑91   CGGTCGGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGCCCCGTAATCACGGAACTCTTTT                                                                                                 <  1:571593/91‑1   CGGTCGGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCAGTACCAAACAAAAGAGTTCCGTGATTATGGGTCTCTTTT                                                                                                 <  1:5431399/91‑1    GGTCGGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTTTTT                                                                                                >  1:731826/1‑91    GGTCGGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTTTTT                                                                                                >  1:728459/1‑91    GGTCGGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTTTTT                                                                                                >  1:1880979/1‑91     GTCGGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTTTTTG                                                                                               >  1:4300092/1‑91     GTCGGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTTTTTG                                                                                               <  1:1461954/91‑1      TCGGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTTTTTGT                                                                                              >  2:1668528/1‑91      TCGGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTTTTTGT                                                                                              <  2:1214536/91‑1      TCGGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTTTTTGT                                                                                              <  2:1684592/91‑1      TCGGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTTTTTGT                                                                                              <  2:3077270/91‑1      TCGGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTTTTTGT                                                                                              <  2:4061439/91‑1      TCGGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTTTTTGT                                                                                              >  1:5525579/1‑91      TCGGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTTTTTGT                                                                                              >  2:89251/1‑91      TCGGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTTTTTGT                                                                                              <  1:3696197/91‑1        GGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTTTTTGTTT                                                                                            <  1:1358773/91‑1        GGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTTTTTGTTT                                                                                            <  1:1358798/91‑1        GGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTTTTTGTTT                                                                                            >  2:2163426/1‑91        GGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTTTTTGTTT                                                                                            >  2:4536142/1‑91        GGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTTTTTGTTT                                                                                            <  1:1414154/91‑1        GGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTTTTTGTTT                                                                                            <  1:365760/91‑1                                                          CCAAACAAAAGAGTTCCGTGATTACGGGGCTCTTTTTGTTTGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTCGAACCC                                          >  1:5518260/1‑91                                                             AACAAAAGAGTTCCGTGATTACGGGGCTCTTTTTGTTTGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTCGAACCCCCG                                       >  1:2956759/1‑91                                                                AAAAGAGTTCCGTGATTACGGGGCTC‑TTTTGTTTGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTCGAACCCCCGACCG                                   >  1:5480047/1‑91                                                                   AGAGTTCCGTGATTACGGGGCTCTTTTTGTTTGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTCGAACCCCCGACCGAT                                 >  2:605762/1‑91                                                                   AGAGTTCCGTGATTACGGGGCTCTTTTTGTTTGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTCGAACCCCCGACCGAT                                 >  2:5263175/1‑91                                                                    GAGTTCCGTGATTACGGGGCTCTTTTTGTTTGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTCGAACCCCCGACCGATG                                >  1:727965/1‑91                                                                    GAGTTCCGTGATTACGGGGCTCTTTCTGTGTGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGTATTCGAACCCACGACCGATG                                >  2:4740548/1‑91                                                                     AGTTCCGTGATTACGGGGCTCTTTTTGTTTGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTCGAACCCCCGACCGATGG                               >  2:43793/1‑91                                                                     AGTTCCGTGATTACGGGGCTC‑TTTTGTTTGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTCGAACCCCCGACCGATGGC                              >  2:4894533/1‑91                                                                     AGTTCCGTGATTACGGGGCTC‑TTTTGTTTGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTCGAACCCCCGACCGATGGC                              >  1:385895/1‑91                                                                      GTTCCGTGATTACGGGGCTCTTTTTGTTTGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTCGAACCCCCGACCGATGGC                              >  2:4116321/1‑91                                                                      GTTCCGTGATTACGGGGCTCTTTTTGTTTGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTCGAACCCCCGACCGATGGC                              >  2:3815536/1‑91                                                                         CCGTGATTACGGGGCTC‑TTTTGTTTGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTCGAACCCCCGACCGATGGCTTAG                          >  1:2598343/1‑91                                                                                           TTTTGTTTGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTCGAACCCCCGACCGATGGCTTAGAAGGCCATTGCTCTATC         <  1:4539331/91‑1                                                                                           TTTTGTTTGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTCGAACCCCCGACCGATGGCTTAGAAGGCCATTGCTCTATC         >  2:3393740/1‑91                                                                                            TTTGTTTGGTGATGCGTATAAAAATACCTATAAGCGTCCTGGGAGGGATTCGAACCCCCGACCGATGGCTCAGAAGGCCATTGCTCTATCC        <  1:5157984/91‑1                                                                                            TTTGTTTGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTCGAACCCCCGACCGATGGCTTAGAAGGCCATTGCTCTATCC        >  1:527149/1‑91                                                                                            TTTGTTTGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTCGAACCCCCGACCGATGGCTTAGAAGGCCATTGCTCTATCC        <  1:3724738/91‑1                                                                                            TTTGTTTGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTCGAACCCCCGACCGATGGCTTAGAAGGCCATTGCTCTATCC        >  1:2480621/1‑91                                                                                            TTTGTTTGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTCGAACCCCCGACCGATGGCTGAGAAGGCCATTGCTCTATCC        <  1:5157518/91‑1                                                                                             TTGTTTGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTCGAACCCCCGACCGATGGCTTAGAAGGCCATTGCTCTATCCA       >  2:3190932/1‑91                                                                                             TTGTTTGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTCGAACCCCCGACCGATGGCTTAGAAGGCCATTGCTCTATCCA       >  1:1973578/1‑91                                                                                              TGTTTGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTCGAACCCCCGACCGATGGCTTAGAAGGCCATTGCTCTATCCAG      <  2:2754547/91‑1                                                                                               GTTTGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTCGAACCCCCGACCGATGGCTTAGAAGGCCATTGCTCTATCCAGC     >  1:2676317/1‑91                                                                                               GTTTGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTCGAACCCCCGACCGATGGCTTAGAAGGCCATTGCTCTATCCAGC     <  2:2085761/91‑1                                                                                               GTTTGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTCGAACCCCCGACCGATGGCTTAGAAGGCCATTGCTCTATCCAGC     <  1:2710151/91‑1                                                                                               GTTTGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTCGAACCCCCGACCGATGGCTTAGAAGGCCATTGCTCTATCCAGC     >  1:4200856/1‑91                                                                                               GTTTGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTCGAACCCCCGACCGATGGCTTAGAAGGCCATTGCTCTATCCAGC     <  1:4534367/91‑1                                                                                               GTTTGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTCGAACCCCCGACCGATGGCTTAGAAGGCCATTGCTCTATCCAGC     <  2:3306618/91‑1                                                                                                 TTGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTCGAACCCCCGACCGATGGCTTAGAAGGCCATTGCTCTATCCAGCTG   <  1:2371344/91‑1                                                                                                 TTGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTCGAACCCCCGACCGATGGCTTAGAAGGCCATTGCTCTATCCAGCTG   <  1:3829898/91‑1                                                                                                  TGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTCGAACCCCCGACCGATGGCTTAGAAGGCCATTGCTCTATCCAGCTGA  <  1:1938178/91‑1                                                                                                  TGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTCGAACCCCCGACCGATGGCTTAGAAGGCCATTGCTCTATCCAGCTGA  >  1:3635503/1‑91                                                                                                  TGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTCGAACCCCCGACCGATGGCTTAGAAGGCCATTGCTCTATCCAGCTGA  >  2:379913/1‑91                                                                                                  TGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTCGAACCCCCGACCGATGGCTTAGAAGGCCATTGCACTATCCAGCTGA  >  2:3750748/1‑91                                                                                                                                                                                              ATCGGTCGGGGGTTCGAATCCCTCCCAGGACGTTTATAGGTATTTTTATACGCATTACCAAACAAAAGAGTTCCGTGATTACGGGGCTCTTTTTGTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/1181939‑1181842 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttttgtttGGTAATGCGTATAAAAATACCTATAAACGTCCTGGGAGGGATTCGAACCCCCGACCGATGGCTTAGAAGGCCATTGCTCTATCCAGCTGA  >  USA300TCH1516_ALE/1181881‑1181970

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