New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1822873	144 (0.710)	15 (0.080)	8/142	NT	9.6%	intergenic (+194/+52)	USA300HOU_RS09070/ackA	Putative universal stress protein/Acetate kinase
	?	USA300TCH1516_ALE	= 1822899	154 (0.850)					intergenic (+220/+26)	USA300HOU_RS09070/ackA	Putative universal stress protein/Acetate kinase

TAATGTTTTCATAATCTTCTTCGACTACTTAATTCTTTAAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGCGTCTA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1822775‑1822873 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aagcgtctaTCTCCGCTACAATTATATGTAGGAGGTAGACGCTTTTTGTATTGTTTGAAAATTAACTAGTGTAATGTCTCTTTTCACGAATATCTTAA  <  USA300TCH1516_ALE/1822899‑1822811                                                                                                                                                                                              TAATGTTTTCATAATCTTCTTCGACTACTTAATTCTTTAAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAA                                                                                                   <  1:2302145/91‑1  AATGTTTTCATAATCTTCTTCGACTACTTAATTCTTTAAGATATTCGTGAAAAGAGCCATTACACTAGTTAATTTTCAAACAATACAAAAA                                                                                                  >  2:3335317/1‑91  AATGTTTTCATAATCTTCTTCGACTACTTAATTCTTTAAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAA                                                                                                  >  2:3336255/1‑91  AATGCTATCATAATCTTCTTCGACTACTTAATTCTTTAAGATATTCATGAAAACAGACATTACACTAGTTAATTTTCAAACAATACAAAAA                                                                                                  >  2:3335353/1‑91    TGTTTTCATAATCTTCTTTGACTACTTAATTCTTTAAGATATTCTTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGC                                                                                                <  1:3142097/91‑1    TGTTTTCATAATCTTCTTCGACTACTTAATTCTTTAAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGC                                                                                                >  1:3919460/1‑91    TGTTTTCATAATCTTCTTCGACTACTTAATTCTTTAAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGC                                                                                                >  1:3919425/1‑91    TGTTTTCATAATCGTCTTTGACGACTTAATTCTTTAAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGC                                                                                                <  1:1137202/91‑1     GTTTTCATCATCTTCTTCGACTACTTAATTCTTTAAGATATTCGTGAAAAGAGACATTACAGTAGTTAATTTTCAAACAATACAAAAAGCG                                                                                               <  2:3441599/91‑1     GTTTTCATAATCTTCTTCGACTACTTAATTCTTTAAGATATTCGTGAATAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGCG                                                                                               >  2:2697792/1‑91     GTTTTCATAATCTTCTTCGACTACTTAATTCTTTAAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGCG                                                                                               <  2:472563/91‑1     GTTTTCATAATCTTCTTCGACTACTTAATTCTTTAAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGCG                                                                                               >  2:2697692/1‑91      TTTTCATAATCTTCTTCGACTACTTAATTCTTTAAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAATAGCGT                                                                                              >  2:3638111/1‑91      TTTTCATAATCTTCTTCGACTACTTAATTCTTTAAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGCGT                                                                                              >  2:3501778/1‑91      TTTTCATAATCTTCTTCGACTACTTAATTCTTTAAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGCGT                                                                                              >  2:52843/1‑91      TTTTCATAATCTTCTTCGACTACTTAATTCTTTAAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGCGT                                                                                              <  1:3832277/91‑1      TTTTCATAATCTTCTTCGACTACTTAATTCTTTAAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGCGT                                                                                              <  1:2176666/91‑1      TTTTCATAATCTTCTTCGACTACTTAATTCTTTAAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGCGT                                                                                              <  2:2199131/91‑1      TTTTCATAATCTTCTTCGACTACTTAATTCTTTAAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGCGT                                                                                              >  2:832090/1‑91      TTTTCATAATCTTCTTCGACTACTTAATTCTTTAAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGCGT                                                                                              >  2:1044580/1‑91      TTTTCATAATCTTCGACGACTACTTAATTCTTTAAGATAATCATGAAAAGAGACATTACACTAGTTAATTTTAAAAAAAAAAAAAAAGCGT                                                                                              <  2:300288/91‑1       TTTCATAATCTTCTTCGACTACTTAATTCTTTAAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGCGTC                                                                                             <  1:2286801/91‑1       TTTCATAATCTTCTTCGACTACTTAATTCTTTAAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGCGTC                                                                                             >  2:2669533/1‑91       TTTCATAATCTTCTTCGACTACTTAATTCTTTAAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGCGTC                                                                                             <  2:3085830/91‑1        TTCATAATCTTCTTCGACTACTTAATTCTTTAAGATATTCGTGAAAAGAGACATTACCCTAGTTAATTTTCAAACAATACAAAAAGCGTCT                                                                                            >  2:3228839/1‑91        TTCATAATCTTCTTCGACTACTTAATTCTTTAAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGCGTCT                                                                                            >  2:1913119/1‑91        TTCATAATCTTCTTCGACTACTTAATTCTTTAAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGCGTCT                                                                                            <  2:2065837/91‑1        TTCATAATCTTCTTCGACTACTTAATTCTTTAAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGCGTCT                                                                                            <  2:261323/91‑1        TTCATAATCTTCTTCGACTACTTAATTCTTTAAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGCGTCT                                                                                            >  2:3546413/1‑91          CATAATCTTCTTCGACTACTTAATTCTTTAAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTGCAAACAACACAAAAAGCGTCTca                                                                                          >  2:697714/1‑89              ATCTTCTTCGACTACATAATTCTTTAAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGCGTCTAGCTCC                                                                                      <  1:1575168/91‑1                                 TTCTTTAAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGCGTCTATCTCCGCTACAATTATATGTAGGA                                                                   <  2:3100982/91‑1                                 TTCTTTAAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGCGTCTATCTCCGCTACAATTATATGTAGGA                                                                   <  2:485362/91‑1                                    TTTAAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGCGTCTATCTCCGCTACAATTATATGTAGGAGGT                                                                <  2:1555152/91‑1                                    TTTAAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGCGTCTATCTCCGCTACAATTATATGTAGGAGGT                                                                <  2:3376342/91‑1                                    TTTAAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGCGTCTATCTCCGCTACAATTATATGTAGGAGGT                                                                <  1:2883685/91‑1                                     TTAAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGCGTCTATCTCCGCTACAATTATATGTAGGAGGTA                                                               <  2:2783107/91‑1                                      TAAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGCGTCTATCTCCGCTACAATTATATGTAGGAGGTAG                                                              <  2:963223/91‑1                                      TAAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGCGTCTATCTCCGCTACAATTATATGTAGGAGGTAG                                                              <  1:1153632/91‑1                                       AAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGCGTCTATCTCCGCTACAATTATATGTAGGAGGTAGA                                                             <  2:3803302/91‑1                                       AAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGCGTCTATCTCCGCTACAATTATATGTAGGAGGTAGA                                                             <  1:2712248/91‑1                                       AAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGCGTCTATCTCCGCTACAATTATATGTAGGAGGTAGA                                                             <  1:669224/91‑1                                       AAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGCGTCTATCTCCGCTACAATTATATGTAGGAGGTAGA                                                             <  1:881499/91‑1                                         GATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGCGTCTATCTCCGCTACAATTATATGTAGGAGGTAGACG                                                           <  1:2238105/91‑1                                              TCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGCGTCTATCTCCGCTACAATTATATGTAGGAGGTAGACGCTTTT                                                      <  1:1446930/91‑1                                                      AGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGCGTCTATCTCCGCTACAATTATATGTAGGAGGTAGACGCTTTTTGTATTGT                                              <  1:2618230/91‑1                                                                                           AAGCGTCTATCTCCGCTACAATTATATGTAGGAGGTAGACGCTTTTTGTATTGTTTGAAAATTAACTAGTGTAATGTCTCTTTTCACGAAT         >  1:2875485/1‑91                                                                                            AGCGTCTATCTCCGCTACAATTATATGTAGGAGGTAGACGCTTTTTGTATTGTTTGAAAATTAACTAGTGTAATGTCTCTTTTCACGAATA        >  2:3415819/1‑91                                                                                            AGCGTCTATCTCCGCTACAATTATATGTAGGAGGTAGACGCTTTTTGTATTGTTTGAAAATTAACTAGTGTAATGTCTCTTTTCACGAATA        >  2:1997185/1‑91                                                                                             GCGTCTATCTCCGCTACAATTATATGTAGGAGGTAGACGCTTTTTGTATTGTTTGAAAATTAACTAGTGTAATGTCTCTTTTCACGAATAT       >  1:3604788/1‑91                                                                                             GCGTCTATCTCCGCTACAATTATATGTAGGAGGTAGACGCTTTTTGTATTGTTTGAAAATTAACTAGTGTAATGTCTCTTTTCACGAATAT       >  2:3043131/1‑91                                                                                             GCGTCTATCTCCGCTACAATTATATGTAGGAGGTAGACGCTTTTTGTATTGTTTGAAAATTAACTAGTGTAATGTCTCTTTTCACGAATAT       <  2:676327/91‑1                                                                                             GCGTCTATCTCCGCTACAATTATATGTAGGAGGTAGACGCTTTTTGTATTGTTTGAAAATTAACTAGTGTAATGTCTCTTTTAACGAATAa       >  1:2269893/1‑90                                                                                              CGTCTATCTCCGCTACAATTATATGTAGGAGGTAGACGCTTTTTGTATTGTTTGAAAATTAACTAGTGTAATGTCTCTTTTCACGAATATC      >  2:2916099/1‑91                                                                                              CGTCTATCTCCGCTACAATTATATGTAGGAGGTAGACGCTTTTTGTATTGTTTGAAAATTAACTAGTGTAATGTCTCTTTTCACGAATATC      >  2:1219935/1‑91                                                                                              CGTCTATCTCCGCTACAATTATATGTAGGAGGTAGACGCTTTTTGTATTGTTTGAAAATTAACTAGTGTAATGTCTCTTTTCACGAATATC      >  2:1624411/1‑91                                                                                              CGTCTATCTCCGCTACAATTATATGTAGGAGGTAGACGCTTTTTGTATTGTTTGAAAATTAACTAGTGTAATGTCTCTTTTCACGAATATC      >  1:911889/1‑91                                                                                              CGTCTATCTCCGCTACAATTATATGTAGGAGGTAGACGCTTTTTGTATTGTTTGAAAATTAACTAGTGTAATGTCTCTTTTCACGAATATC      >  2:185139/1‑91                                                                                               GTCTATCTCCGCTACAATTATATGTAGGAGGTAGACGCTTTTTGTATTGTTTGAAAATTAACTAGTGTAATGTCTCTTTTCACGAATATCT     <  2:1296486/91‑1                                                                                               GTCTATCTCCGCTACAATTATATGTAGGAGGTAGACGCTTTTTGTATTGTTTGAAAATTAACTAGTGTAATGTCTCTTTTCACGAATATCT     <  1:1518478/91‑1                                                                                                 tgATCTCCGCTACAGTTATATGTAGGAGGTAGACGCTTTTTGTATTGTTTGAAAATTAACTAGTGTAATGTCTCTTTTCACGAGTATCTTA   <  2:478253/89‑1                                                                                                 CTATCTCCGCTGCAATTATATGTCGGAGGTAGACGCTTTTTGTATTGTTTGAAAATTAAGTAGTGTAATGTCTCTTTTCACGAATATCTTA   <  2:3017066/91‑1                                                                                                 CTATCTCCGCTACAATTATATGTAGGAGGTAGACGCTTTTTGTATTGTTTGAAAATTAACTAGTGTAATGTCTCTTTTCACGAATATCTTA   >  2:433189/1‑91                                                                                                  TATCTCCGCTACAATTATATGTAGGAGGTAGACGCTTTTTGTATTGTTTGAAAATTAACTAGTGTAATGTCTCTTTTCACGAATATCTTAA  >  1:2225452/1‑91                                                                                                  TATCTCCGCTACAATTATATGTAGGAGGTAGACGCTTTTTGTATTGTTTGAAAATTAACTAGTGTAATGTCTCTTTTCACGAATATCTTAA  >  2:451066/1‑91                                                                                                  TATCTCCGCTACAATTATATGTAGGAGGTAGACGCTTTTTGTATTGTTTGAAAATTAACTAGTGTAATGTCTCTTTTCACGAATATCTTAA  <  1:914412/91‑1                                                                                                                                                                                              TAATGTTTTCATAATCTTCTTCGACTACTTAATTCTTTAAGATATTCGTGAAAAGAGACATTACACTAGTTAATTTTCAAACAATACAAAAAGCGTCTA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1822775‑1822873 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aagcgtctaTCTCCGCTACAATTATATGTAGGAGGTAGACGCTTTTTGTATTGTTTGAAAATTAACTAGTGTAATGTCTCTTTTCACGAATATCTTAA  <  USA300TCH1516_ALE/1822899‑1822811

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.